Compositions and methods for improving mitochondrial function

ABSTRACT

Provided herein are methods and compositions comprising a bacterium or a metabolite thereof for enhancing mitochondrial and/or peroxisomal function.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of PCT Application No. PCT/US2019/014725, filed Jan. 23, 2019, which claims benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 62/620,641, filed Jan. 23, 2018 and U.S. Provisional Application No. 62/721,979, filed Aug. 23, 2018, the contents of each of which are incorporated herein by reference in their entirety.

GOVERNMENT SUPPORT

This invention was made with government support under Grant No. AG043181-16A, awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The field of the invention relates to bacterial compositions or bacterial extracts for the treatment of a symptom of a disease associated with mitochondrial dysfunction.

BACKGROUND

Mitochondria play a crucial role in ATP generation, fatty acid β-oxidation, catabolism of amino acids, ketogenesis, generation of reactive oxygen species (ROS) and calcium homeostasis. Mitochondrial dysfunction is associated with a number of human diseases, including neurological and muscular degeneration, cardiovascular disorders, obesity, diabetes, and conditions such as aging. Mitochondria contribute to aging through decreased ATP production, increased ROS production, and activation of apoptotic pathways. Decreases in mitochondrial energy production combined with increased oxidative stress, play a causal role in several neurodegenerative disease including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Also, aging is by far the greatest risk factor for several of these neurodegenerative diseases. Regardless of whether a primary or secondary cause, mitochondrial dysfunction holds promise as a target for identifying therapeutics for neurodegenerative diseases. With the increasing average life expectancy worldwide, the number of people affected by aging related decline in mitochondrial function will rise considerably in the near future. Thus, there is a significant clinical unmet need for new therapeutic approaches that not only can be used to slow neurodegenerative diseases but also as preventive measures for protecting or improving mitochondrial function in the aging population.

SUMMARY

The methods, compositions and treatments described herein are based, in part, on the discovery of a bacterial extract or bacterial composition that improves mitochondrial function by, for example, increasing production of intracellular energy (e.g., ATP). Accordingly, provided herein are bacterial extracts and compositions for the treatment of mitochondrial dysfunction associated with metabolic disorders, neurodegenerative disorders (e.g., Parkinson's disease, among others) and peroxisomal disorders.

The present invention relates generally to the use of members of live or inactivated Acetobacteriaceae family microbes, a microbial combination, an extract, active fraction or metabolites, or a combination thereof for promoting, enhancing and/or restoring mitochondrial function. Such compositions can be used for treatment or prevention of diseases, developmental delays, and symptoms related to mitochondrial dysfunction, such as aging, metabolic disorders, muscular disorders and neurodegenerative diseases.

Provided herein in one aspect is a composition comprising a measured amount of one or more bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In one embodiment of this aspect and all other aspects described herein, the bacterium is from the Acetobacteriaceae family.

In another embodiment of this aspect and all other aspects described herein, the bacterium is Gluconobacter spp, Acetobacter spp., Gluconoacaetobacter spp., Acidomonas spp, Ameyamaea spp., Asaia spp., Granulibacter spp., Kozakia spp., Neoasaia spp., Neokomagataea spp., Saccharibacter spp., Swaminathania spp., or Tanticharoenia spp. or combination of two or more of these (e.g., a combination of three or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, or 12 or more of these).

In another embodiment of this aspect and all other aspects described herein, the bacterium is Gluconobacter albidus, Gluconobacter cerinus, Gluconobacter frateruii, Gluconobacter japonicus, Gluconobacter kondonii, Gluconobacter nephelii, Gluconobacter oxydans, Gluconoacetobacter diazotrophicus, Gluconoacetobacter hansenii, Gluconoacetobacter saccharivorans, Acetobacter aceti or Acetobacter malorum. In another embodiment of this aspect and all other aspects provided herein, the bacterium is Gluconobacter EBT 405. In another embodiment, the composition comprises at least two or more, at least three or more, at least four or more, at least five or more, at least six or more, at least seven or more, at least eight or more, at least nine or more, at least ten or more, at least eleven or more, at least twelve (or each of) these bacterial species.

In another embodiment of this aspect and all other aspects described herein, one or more of the nucleic acid sequences are exogenous nucleic acid sequences.

In another embodiment of this aspect and all other aspects described herein, the bacterium comprises and expresses nucleic acid sequences encoding each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects described herein, the measured amount of the one or more bacterium is lyophilized.

In another embodiment of this aspect and all other aspects described herein, the measured amount is an amount effective to induce expression and/or activity of mitochondrial transcription factor A (TFAM), or peroxisome proliferator activated receptor gamma coactivator 1 (PGC) in a human cell upon administration to a subject in need thereof.

In another embodiment of this aspect and all other aspects described herein, the amount effective to induce expression and/or activity of TFAM, or PGC in a human cell is 1×10⁶ bacteria.

In another embodiment of this aspect and all other aspects described herein, the composition further comprises one or more added bacterial metabolites selected from the group consisting of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects described herein, the bacterium is viable, attenuated or heat-inactivated.

In another embodiment of this aspect and all other aspects described herein, the composition is formulated as a food, a beverage, a feed composition, a probiotic, a nutritional supplement, or a pharmaceutical composition.

In another embodiment of this aspect and all other aspects described herein, the composition further comprises a prebiotic.

In another embodiment of this aspect and all other aspects described herein, the prebiotic comprises a fructooligosaccharide, an inulin, an isomaltooligosaccharide, lactilol, lactosucrose, lactulose, a soy oligosaccharide, a transgalactooligosaccharide or a xylooligosaccharide,

In another embodiment of this aspect and all other aspects described herein, the composition further comprises a pharmaceutically acceptable carrier.

In another embodiment of this aspect and all other aspects described herein, the composition is formulated for oral administration.

In another embodiment of this aspect and all other aspects described herein, the composition is an enteric-coated formulation.

Another aspect provided herein relates to a composition comprising a therapeutically effective amount of an extract or fraction derived from at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding an enzyme selected from the group consisting of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In one embodiment of this aspect and all other aspects provided herein, the at least one bacterium comprises and expresses each of the enzymes membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the extract or fraction comprises one or more metabolites selected from gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the extract or fraction is from bacterial cells cultured in a medium comprising: (i) standard Lysogeny broth (1% tryptone, 0.5% yeast extract, and 1% sodium chloride) containing 1% glucose, (ii) standard Hestrin-Schramm broth (D-glucose 2%, 0.5% yeast extract, 0.5% peptone, 0.27% disodium phosphate, 0.115% citric acid) or (iii) CaCO₃ medium comprising 8% glucose, 0.5% yeast extract, 0.2% mannitol, 0.05% magnesium sulphate, and 10% calcium carbonate.

In another embodiment of this aspect and all other aspects provided herein, the extract or fraction comprises metabolites or bacterial byproducts that promote ATP production in at least one cell type of a host mammal administered the composition.

In another embodiment of this aspect and all other aspects provided herein, the extract or fraction does not comprise viable bacterial cells.

In another embodiment of this aspect and all other aspects provided herein, the extract or fraction lacks detectable bacteria.

In another embodiment of this aspect and all other aspects provided herein, the extract or fraction further comprises attenuated or heat-inactivated bacteria.

In another embodiment of this aspect and all other aspects provided herein, the bacterium is from the Acetobacteriaceae family.

In another embodiment of this aspect and all other aspects provided herein, the bacterium is Gluconobacter spp, Acetobacter spp., Gluconoacaetobacter spp., Acidomonas spp, Ameyamaea spp., Asaia spp., Granulibacter spp., Kozakia spp., Neoasaia spp., Neokomagataea spp., Saccharibacter spp., Swaminathania spp., or Tanticharoenia spp. or combination of two or more of these (e.g., a combination of three or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, or 12 or more of these).

In another embodiment of this aspect and all other aspects described herein, the bacterium is Gluconobacter albidus, Gluconobacter cerinus, Gluconobacter frateruii, Gluconobacter japonicus, Gluconobacter kondonii, Gluconobacter nephelii, Gluconobacter oxydans, Gluconoacetobacter diazotrophicus, Gluconoacetobacter hansenii, Gluconoacetobacter saccharivorans, Acetobacter aceti or Acetobacter malorum. In another embodiment of this aspect and all other aspects provided herein, the bacterium is Gluconobacter EBT 405. In another embodiment, the composition comprises at least two or more, at least three or more, at least four or more, at least five or more, at least six or more, at least seven or more, at least eight or more, at least nine or more, at least ten or more, at least eleven or more, at least twelve (or each of) these bacterial species.

In another embodiment of this aspect and all other aspects provided herein, one or more of the nucleic acid sequences is/are an exogenous nucleic acid sequence(s).

In another embodiment of this aspect and all other aspects provided herein, the composition is formulated as a food, a beverage, a feed composition, a nutritional supplement, or a pharmaceutical composition.

In another embodiment of this aspect and all other aspects provided herein, the composition further comprises a pharmaceutically acceptable carrier.

In another embodiment of this aspect and all other aspects provided herein, the composition is formulated for oral administration.

Also provided herein, in another aspect, is a method for increasing cellular ATP production in at least one cell type of a subject in need thereof, the method comprising administering to the subject a composition comprising an amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, effective to increase cellular ATP production in at least one cell type.

In one embodiment of this aspect and all other aspects provided herein, the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, one or more of the nucleic acid sequences is exogenous to the bacterium.

In another embodiment of this aspect and all other aspects provided herein, the activity of complex I and/or complex II of the mitochondrial electron transport chain is increased in the one or more cell types.

In another embodiment of this aspect and all other aspects provided herein, the administering increases mitochondrial membrane potential.

In another embodiment of this aspect and all other aspects provided herein, the subject is human.

In another embodiment of this aspect and all other aspects provided herein, expression of peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1a), and/or mitochondrial transcription factor A (TFAM) is increased.

In another embodiment of this aspect and all other aspects provided herein, AMP-activated protein kinase (AMPK) phosphorylation levels, nuclear respiratory factor-2 (Nrf2) protein levels, PGCα mRNA levels TFAM mRNA levels and/or mitochondrial DNA replication is increased.

In another embodiment of this aspect and all other aspects provided herein, the mitochondrial DNA copy number (mtDNA) is increased.

In another embodiment of this aspect and all other aspects provided herein, the method increases the developmental growth rate of a subject carrying a mutations in mitochondrial respiratory Complex I NADH:ubiquinone reductase.

In another embodiment of this aspect and all other aspects provided herein, the expression of at least one mitochondrial β-oxidation enzyme is increased.

In another embodiment of this aspect and all other aspects provided herein, the at least one mitochondrial β-oxidation enzyme is B0303.3, cpt-2, cpt-1, ech-1.2, or acdh-7.

In another embodiment of this aspect and all other aspects provided herein, the longevity of the subject is increased.

In another embodiment of this aspect and all other aspects provided herein, mitochondrial biogenesis is maintained or increased.

In another embodiment of this aspect and all other aspects provided herein, cellular ATP production is increased by at least 10% compared to the cellular ATP production prior to administration of the composition.

Another aspect provided herein relates to a method for making a bacterial extract, the method comprising culturing at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II in a medium comprising: (i) standard Lysogeny broth (1% tryptone, 0.5% yeast extract, and 1% sodium chloride) containing 1% glucose, (ii) standard Hestrin-Schramm broth (D-glucose 2%, 0.5% yeast extract, 0.5% peptone, 0.27% disodium phosphate, 0.115% citric acid) or (iii) CaCO₃ medium comprising 8% glucose, 0.5% yeast extract, 0.2% mannitol, 0.05% magnesium sulphate, and 10% calcium carbonate.

In one embodiment of this aspect and all other aspects provided herein, the at least one bacterium comprises and expresses nucleic acid sequences encoding each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

Also provided herein, in another aspect, is a composition comprising an amount of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid effective to increase cellular ATP production in at least one cell type of a host mammal administered the composition.

Another aspect provided herein relates to a composition comprising an amount of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid effective to increase the expression and/or activity of mitochondrial transcription factor A (TFAM), or peroxisome proliferator activated receptor gamma coactivator 1 (PGC) in at least one cell type of a human subject administered the composition.

In one embodiment of this aspect and all other aspects provided herein, the composition comprises a bacterial extract or active fraction thereof.

In another embodiment of this aspect and all other aspects provided herein, the composition is formulated as a food, a beverage, a feed composition, a nutritional supplement, or a pharmaceutical composition.

Provided herein, in another aspect, is a method of treating Parkinson's disease, the method comprising administering to a subject having Parkinson's disease, a composition comprising a therapeutically effective amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, thereby reducing at least one symptom of Parkinson's disease.

In one embodiment of this aspect and all other aspects provided herein, the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one symptom is selected from the group consisting of: tremor, sleep disturbance, mobility impairment, involuntary movement, muscle rigidity, rhythmic muscle contraction, slow bodily movement, slow shuffling gait, fatigue, dizziness, impaired balance, restlessness, amnesia, confusion, dementia, cognitive impairment, impaired speech, anxiety, apathy, distorted or loss of sense of smell, urinary incontinence, reduced facial expression, weight loss and constipation.

In another embodiment of this aspect and all other aspects provided herein, the bacterium is Gluconobacter EBT 405.

Another aspect provided herein relates to a method of treating a mitochondrial electron transport chain disorder, the method comprising administering to a subject having a mitochondrial electron transport chain disorder, a composition comprising a therapeutically effective amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, thereby reducing at least one symptom of the mitochondrial electron transport chain disorder.

In one embodiment of this aspect and all other aspects provided herein, the mitochondrial electron transport chain disorder comprises a disorder or impaired activity in Complex I and/or Complex II.

In another embodiment of this aspect and all other aspects provided herein, the mitochondrial electron transport chain disorder is NADH dehydrogenase (NADH-CoQ reductase) deficiency, succinate dehydrogenase deficiency, Leigh Disease, mitochondrial DNA depletion, or mitochondrial insufficiency.

In another embodiment of this aspect and all other aspects provided herein, the at least one symptom is selected from the group consisting of: myopathy, mitochondrial encephalomyopathy, failure to thrive, developmental delay, hypotonia, lethargy, respiratory failure, ataxia, myoclonus, lactic acidosis, seizures, fatigue, nystagmus, poor reflexes, difficulty eating or swallowing, breathing difficulties, ataxia, congenital myopathy, infantile myopathy and hepatopathy.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

Another aspect provided herein relates to a method of treating a peroxisomal disorder, the method comprising administering to a subject having a peroxisomal disorder, a composition comprising a therapeutically effective amount of at least one bacterium that comprises one or more nucleic acid sequences such that the bacterium expresses the following enzymes: membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or a bacterial extract thereof, thereby reducing at least one symptom of the peroxisomal disorder.

In another embodiment of this aspect and all other aspects provided herein, the peroxisomal disorder is Zellweger syndrome spectrum (PBD-ZSD), or rhizomelic chondrodysplasia punctate type 1 (RCDP1).

In another embodiment of this aspect and all other aspects provided herein, the PBD-ZSD is infantile Refsum disease, neonatal adrenoleukodystrophy, or Zellweger syndrome.

In another embodiment of this aspect and all other aspects provided herein, the at least one symptom is selected from the group consisting of: skeletal and craniofacial dysmorphism, liver dysfunction, progressive sensorineural hearing loss and retinopathy.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

Also provided herein, in another aspect, is a method for increasing the biogenesis of cellular mitochondria or peroxisomes, the method comprising administering to a subject, a composition comprising an amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or a fraction or extract thereof, effective to increase the biogenesis of cellular mitochondria or peroxisomes.

In one embodiment of this aspect and all other aspects provided herein, the size and/or number of peroxisomes is increased.

In one embodiment of this aspect and all other aspects provided herein, mitochondrial activity is increased.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium expresses each of encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

Also provided herein, in another aspect, is a method of treating Alzheimer's disease, the method comprising administering to a subject having Alzheimer's disease, a composition comprising a therapeutically effective amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, thereby reducing at least one symptom of Alzheimer's disease.

In one embodiment of this aspect and all other aspects provided herein, the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

In another embodiment of this aspect and all other aspects provided herein, the at least one symptom is selected from the group consisting of: cognitive decline, confusion, delusion, disorientation, forgetfulness, difficulty concentrating, inability to generate new memories, inability to do simple math, inability to recognize common items, aggression, agitation, irritability, meaningless repetition of own words, personality changes, restlessness, lack of restraint, wandering, anger, apathy, general discontent, loneliness, mood swings, depression, hallucination, paranoia, loss of appetite, inability to combine muscle movements and jumbled speech.

In another embodiment of this aspect and all other aspects provided herein, the bacterium is Gluconobacter EBT 405.

Another aspect provided herein relates to the use of a composition comprising gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid for the treatment of Parkinson's disease or Alzheimer's disease.

Another aspect provided herein relates to the use of composition as described herein in the treatment of Parkinson's disease or Alzheimer's disease.

Another aspect provided herein relates to the use of a composition comprising gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid for increasing cellular ATP production.

Another aspect provided herein relates to the use of a composition as described herein for increasing cellular ATP production.

Another aspect provided herein relates to the use of a composition comprising gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid for treating a mitochondrial electron transport chain disorder or a peroxisomal disorder.

Another aspect provided herein relates to the use of a composition as described herein for the treatment of a mitochondrial electron transport chain disorder or a peroxisomal disorder.

Another aspect provided herein relates to the use of a composition comprising gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid for increasing cellular biogenesis of mitochondria or peroxisomes.

Another aspect provided herein relates to the use of a composition as described herein for increasing cellular biogenesis of mitochondria or peroxisomes.

Another aspect provided herein relates to the use of a composition comprising gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid for increasing the expression and/or activity of TFAM or peroxisome proliferator activated receptor gamma coactivator 1 (PGC-1).

Another aspect provided herein relates to the use of a composition of as described herein for increasing the expression and/or activity of TFAM or peroxisome proliferator activated receptor gamma coactivator 1 (PGC-1).

Another aspect provided herein relates to the use of a composition comprising a measured amount of one or more bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II for the treatment or prevention of Alzheimer's disease or Parkinson's disease.

In one embodiment of this aspect and all other aspects provided herein, the one or more bacterium comprises Gluconobacter EBT 405.

Definitions

The terms “patient,” “subject” and “individual” are used interchangeably herein, and refer to an animal, particularly a human, to whom treatment, including prophylactic treatment is provided. The term “subject” as used herein refers to human and non-human animals. The term “non-human animals” and “non-human mammals” are used interchangeably herein and includes all vertebrates, e.g., mammals, such as non-human primates, (particularly higher primates), sheep, dog, rodent (e.g. mouse or rat), guinea pig, goat, pig, cat, rabbits, cows, and non-mammals such as chickens, amphibians, reptiles etc. In one embodiment, the subject is human. In another embodiment, the subject is an experimental animal or animal substitute as a disease model. In another embodiment, the subject is a domesticated animal including companion animals (e.g., dogs, cats, rats, guinea pigs, hamsters etc.). It is specifically contemplated herein that a subject can be of any developmental age including, but not limited to, a fetus, a neonate, an infant, a toddler, a child, an adolescent, an adult, post-menopausal, or a geriatric subject.

As used herein, a “prebiotic” refers to an ingredient that allows or promotes specific changes, both in the composition and/or activity in the gastrointestinal microbiota that may (or may not) confer benefits upon the host. In some embodiments, a prebiotic can include one or more of the following: fructooligosaccharide, galactooligosaccharides, hemicelluloses (e.g., arabinoxylan, xylan, xyloglucan, and glucomannan), inulin, chitin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, gums (e.g., guar gum, gum arabic and carrageenan), oligofructose, oligodextrose, tagatose, resistant maltodextrins (e.g., resistant starch), trans-galactooligosaccharide, pectins (e.g., xylogalactouronan, citrus pectin, apple pectin, and rhamnogalacturonan-I), dietary fibers (e.g., soy fiber, sugar beet fiber, pea fiber, corn bran, and oat fiber) and xylooligosaccharides.

As used herein, the terms “administering,” “introducing” and “transplanting” are used interchangeably in the context of the placement of cells, e.g., a bacterial composition, as described herein into a subject, by a method or route which results in at least partial localization of the introduced cells at a desired site, such as the intestines or a region thereof, such that a desired effect(s) is produced (e.g., increased mitochondrial ATP production). The cells can be administered by any appropriate route which results in delivery to a desired location in the subject where at least a portion of the delivered cells or components of the cells remain viable. The period of viability of the cells after administration to a subject can be as short as a few hours, e.g., six to twenty-four hours, to a few days, to as long as several years, i.e., long-term engraftment. In some embodiments, the term “administering” refers to the administration of a bacterial extract or preparation comprising one or more bacterial metabolites and/or byproducts but lacking fully viable bacterial cells.

As used herein “preventing” or “prevention” refers to any methodology where the disease state does not occur due to the actions of the methodology (such as, for example, administration of a composition as described herein). In one aspect, it is understood that prevention can also mean that the disease is not established to the extent that occurs in untreated controls. For example, there can be a 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, or 100% reduction in the establishment of disease frequency relative to untreated controls. Accordingly, prevention of a disease encompasses a reduction in the likelihood that a subject will develop the disease, relative to an untreated subject (e.g. a subject who is not treated with a composition as described herein).

“Synergy” or “synergistic interactions” refers to the interaction or cooperation of two or more microbes or metabolites to produce a combined effect greater than the sum of their separate effects. For example, in one embodiment, “synergy” between two or more microbes can result from a first microbe secreting a waste product or metabolite that the second microbe uses to fuel growth or other processes.

The terms “decrease”, “reduced”, “reduction”, or “inhibit” are all used herein to mean a decrease or lessening of a property, level, or other parameter by a statistically significant amount. In some embodiments, “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference level (e.g., the absence of a given treatment) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or more. As used herein, “reduction” or “inhibition” does not encompass a complete inhibition or reduction as compared to a reference level. “Complete inhibition” is a 100% inhibition as compared to a reference level. A decrease can be preferably down to a level accepted as within the range of normal for an individual without a given disorder.

The terms “increased,” “increase” or “enhance” or “activate” are all used herein to generally mean an increase of a property, level, or other parameter by a statistically significant amount; for the avoidance of any doubt, the terms “increased”, “increase” or “enhance” or “activate” means an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, at least about a 20-fold increase, at least about a 50-fold increase, at least about a 100-fold increase, at least about a 1000-fold increase or more as compared to a reference level.

The term “pharmaceutically acceptable” can refer to compounds and compositions which can be administered to a subject (e.g., a mammal or a human) without undue toxicity.

As used herein, the term “pharmaceutically acceptable carrier” can include any material or substance that, when combined with an active ingredient, allows the ingredient to retain biological activity and is substantially non-reactive with the subject's immune system (unless desired). Examples include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution, emulsions such as oil/water emulsion, and various types of wetting agents. The term “pharmaceutically acceptable carriers” excludes tissue culture and bacterial culture media.

As used herein, the term “comprising” means that other elements can also be present in addition to the defined elements presented. The use of “comprising” indicates inclusion rather than limitation.

As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of additional elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the invention.

The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.

Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean±1%.

BRIEF DESCRIPTION OF THE FIGURES

This patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIGS. 1A-1H. FIG. 1A, Gluconoacetobacter feeding suppresses the developmental delay phenotype of spg-7(ad2249), nduf-7(et7), and gas-1(fc21) mutants. FIG. 1B, Gluconoacetobacter feeding increases ATP content in wildtype animals compared to worms fed on E. coli OP50-1 as assessed using a strain that expresses Luciferase in all somatic cells. FIG. 1C, Gluconoacetobacter feeding increases ATP content in wildtype animals compared to worms fed on E. coli OP50-1 as assessed by measuring the endogenous ATP levels using biochemical method. FIG. 1D, Gluconoacetobacter feeding restores the ATP content in spg-7(ad2249) animals to wildtype levels. FIG. 1E, Gluconoacetobacter feeding restores the ATP content in nduf-7(et7) animals to wildtype levels. FIG. 1F, Gluconoacetobacter feeding increases the mitochondrial membrane potential in spg-7(ad2249), nduf-7(et7), and gas-1(fc21) mutants animals compared to the corresponding mutant worms fed on E. coli OP50-1 as assessed using MitoTracker Red CMXRos. FIG. 1G, Animals fed on Gluconacetobacter spp and treated with varying doses of paraquat had significantly higher levels of bioluminescence, a surrogate for ATP levels, compared to animals fed on E. coli OP50 and treated with paraquat. FIG. 1H, Animals fed on Gluconacetobacter spp and treated with varying doses of rotenone had significantly higher levels of bioluminescence, a surrogate for ATP levels, compared to animals fed on E. coli OP50 and treated with rotenone.

FIGS. 2A-2K. FIG. 2A, Worms fed E. coli OP50 and treated with either MPP+ or 6-OHDA or paraquat induced mitochondrial stress reporter hsp-6::gfp expression while worms fed on Gluconacetobacter spp failed to induce the GFP expression. FIG. 2B, Feeding spg-7(ad2249); tbb-6::gfp animals on Gluconacetobacter spp suppressed the activation of tbb-6::gfp expression. FIG. 2C, Gluconoacetobacter feeding suppresses hphd-1::gfp expression. FIG. 2D, Gluconoacetobacter feeding increases B0303.3::gfp expression. FIG. 2E, Gluconoacetobacter feeding increases prx-11::gfp expression. FIG. 2F, tcer-1(RNAi) suppresses the induction of cpt-2::gfp in worms fed on Gluconoacetobacter spp. FIG. 2G, nhr-49(RNAi) suppresses the induction of acox-1.2::gfp in worms fed on Gluconoacetobacter spp. FIG. 2H, tcer-1 (RNAi) suppresses the induction of ech-1.2::gfp in worms fed on Gluconoacetobacter spp. FIG. 2I, nhr-49(RNAi) suppresses the induction of acdh-7::gfp in worms fed on Gluconoacetobacter spp. FIG. 2J, nhr-49(RNAi) suppresses the induction of pmp-4::gfp in worms fed on Gluconoacetobacter spp. FIG. 2K, nhr-49(RNAi) suppresses the induction of prx-6::gfp in worms fed on Gluconoacetobacter spp.

FIGS. 3A-3H. FIG. 3A, tcer-1(tm1452) and nhr-49(nr2041) animals fed on Gluconacetobacter spp feeding grew slower compared to wildtype worms fed on Gluconacetobacter spp. FIG. 3B, RNAi of tcer-1, nhr-49, and prx-5 suppressed the Gluconacetobacter spp feeding induced increase in bioluminescence phenotype. FIG. 3C, nhr-49(RNAi) suppressed the accelerated developmental progression phenotype of spg-7(ad2249) and nduf-7(et19) mutant worms fed on Gluconacetobacter spp. FIG. 3D, prx-5(RNAi) suppressed the accelerated developmental progression phenotype of spg-7(ad2249) and nduf-7(et19) mutant worms fed on Gluconacetobacter spp. FIG. 3E, nhr-49(RNAi) exacerbated the reduced mitochondrial membrane potential of spg-7(ad2249) mutants as assessed using Mito CMXRos. FIG. 3F, Representative picture showing the fused mitochondria phenotype in the muscle of worms fed on Gluconacetobacter spp compared to the worms fed on E. coli OP50 as assessed using a mitochondrially targeted TOM20-RFP fusion protein. FIG. 3G, Representative picture showing increased punctate structures in the intestine of worms fed on Gluconacetobacter spp indicating an increase in peroxisomes as assessed using the peroxisomally targeted GFP-DAF-22 fusion protein. FIG. 3H, Worms fed on Gluconacetobacter spp had slightly lower levels of H₂O₂ indicating that Gluconacetobacter spp as assessed using transgenic worms expressing HyPer sensor.

FIGS. 4A-4I. FIG. 4A, Worms fed on Gluconacetobacter spp had significantly higher levels of bioluminescence, a surrogate for ATP levels, compared to animals fed on E. coli OP50 as the worms age. FIG. 4B, Dilution of Gluconacetobacter spp with E. coli induces significantly higher levels of bioluminescence, a surrogate for ATP levels. FIG. 4C, Gluconacetobacter strains including Gluconacetobacter hanseni (MGH isolate), the canonical Gluconacetobacter hanseni ATCC 23769, and non-cellulose producing mutant of G. hanseni ATCC 23769 induces significantly higher levels of bioluminescence, a surrogate for ATP levels compared worms fed on E. coli OP50. FIG. 4D, Members of Acetobacteraceae induce significantly higher levels of bioluminescence, a surrogate for ATP levels, compared worms fed on E. coli OP50. FIG. 4E, Worms fed on mutants in membrane-bound PQQ-dependent glucose dehydrogenase, cytochrome o ubiquinol oxidase subunit II, and ubiquinol-cytochrome c reductase iron-sulfur subunit have lower levels of bioluminescence, a surrogate for ATP levels, compared to worms fed on wildtype G. oxydans. FIG. 4F, ATP production was decreased in worms fed on deletion mutations in Membrane-bound PQQ-dependent glucose dehydrogenase, FAD-dependent Membrane-bound dehydrogenase, and Membrane-bound PQQ-dependent dehydrogenase 3 compared to worms fed on wildtype G. oxydans. FIG. 4G, PGC-1α gene expression was increased in human primary dermal fibroblasts exposed to Gluconacetobacter spp compared to mock-treated cells as assessed by RT-PCR. FIG. 4H, TFAM gene expression was increased in human primary dermal fibroblasts exposed to Gluconacetobacter spp compared to mock-treated cells as assessed by RT-PCR. FIG. 4I, mtDNA copy numbers were increased in human primary dermal fibroblasts exposed to Gluconacetobacter spp compared to mock-treated cells.

FIGS. 5A-5I. FIG. 5A, Gluconacetobacter spp, Acetobacter spp, and Gluconobacter spp suppresses the developmental delay phenotype of spg-7(ad2249). FIG. 5B, Gluconacetobacter spp, Acetobacter spp, and Gluconobacter spp accelerates the developmental growth rate of wildtype animals compared to the worms fed on E. coli OP50-1. FIG. 5C, Representative picture showing the accelerated developmental growth of wildtype worms fed on Gluconacetobacter spp. FIG. 5D, Wildtype worms fed on Gluconacetobacter spp are slightly longer compared to the worms fed on E. coli OP50-1. Gluconacetobacter spp feeding reduces the time taken for animals to reach egg-laying adult stage from L1-larval stage. FIG. 5E, Gluconacetobacter spp feeding reduces the time taken for animals to reach egg-laying adult stage from L4-larval stage. FIG. 5F, Gluconacetobacter spp induces increase in bioluminescence, a surrogate for ATP production, within 6 hours of initiating feeding with maximal levels by 18 hours of feeding spg-7(ad2249) mutants fed on Gluconacetobacter spp had significantly increased mitochondrial membrane potential compared to animals fed on E. coli OP50 as assessed using TMRE dye. FIG. 5G, Animals fed on Gluconacetobacter spp and treated with rotenone or paraquat or sodium azide had significantly higher levels of bioluminescence, a surrogate for ATP levels, compared to animals fed on E. coli OP50 and treated with rotenone or paraquat or sodium azide. FIG. 5H, spg-7 (ad2249) mutants fed on Gluconacetobacter spp. had significantly increased mitochondrial membrane potential compared to animals fed on E. coli OP50 as assessed using TMRE dye. FIG. 5I, Animals fed on Gluconacetobacter spp and treated with rotenone or paraquat or sodium azide had significantly higher levels of bioluminescence, a surrogate for ATP levels, compared to animals fed on E. coli OP50 and treated with rotenone or paraquat or sodium azide.

FIGS. 6A-6L. FIG. 6A, Animals fed on Gluconacetobacter spp were more resistant to rotenone or paraquat than animals fed on E. coli OP50. FIG. 6B, Feeding spg-7(ad2249); tbb-6::gfp animals on Gluconacetobacter spp suppressed the activation of tbb-6::gfp expression. FIGS. 6C-6G, Gluconoacetobacter feeding increases cpt-2::gfp (FIG. 6C), acox-1.2::gfp (FIG. 6D), pmp-4::gfp (FIG. 6E), acdh-7::gfp (FIG. 6F), ech-1.2::gfp (FIG. 6G) expression compared to worms fed on E. coli OP50. FIG. 6H, Representative figure showing the increased expression of B0303.3::gfp in worms fed on Gluconoacetobacter compared to fed on E. coli OP50. FIG. 6I, Representative figure showing the increased expression of acdh-7::gfp in worms fed on Gluconoacetobacter compared to fed on E. coli OP50. FIG. 6J, Representative figure showing the increased expression of acox-1.2::gfp in worms fed on Gluconoacetobacter compared to those fed on E. coli OP50. FIG. 6K, Representative figure showing the increased expression of cpt-1::gfp in worms fed on Gluconoacetobacter compared to fed on E. coli OP50. FIG. 6L, Representative figure showing no change in expression of rpt-3::gfp in worms fed on Gluconoacetobacter compared to fed on E. coli OP50.

FIGS. 7A-7H. FIG. 7A, Representative figure showing the increased expression of icl-1::gfp in worms fed on Gluconoacetobacter compared to worms fed on E. coli OP50. FIG. 7B, Gluconoacetobacter feeding does not affect fat-7::gfp expression. FIG. 7C, Representative figure showing that Gluconoacetobacter feeding does not affect UbV-gfp expression while treatment with Bortezomib stabilizes UbV-gfp. FIG. 7D, Representative figure showing that Gluconoacetobacter feeding does not induce autophagy while starvation induces autophagy as assessed using the lgg-1::GFP strain. FIG. 7E, Intestine-specific overexpression of nhr-49 was sufficient to accelerate growth rate of nhr-49(nr2041) mutants fed on Gluconacetobacter spp. FIG. 7F, Representative figure showing that the nhr-49 gene expression was induced in the worms fed on Gluconacetobacter spp as assessed using a nhr-49::GFP transcriptional fusion. FIG. 7G, Representative figure showing that TCER-1::GFP expression is increased in the intestinal cell nuclei compared to worms fed on E. coli OP50. FIG. 7H, Representative figure showing that Gluconoacetobacter feeding induces mitochondrial fusion in the hypodermis of worms compared to worms fed on E. coli OP50 as assessed using Rhodamine 6G dye, which stains mitochondria.

FIGS. 8A-8H. FIG. 8A, Representative figure showing that Gluconoacetobacter feeding does not restore the peroxisomal targeting defect in prx-5(RNAi) treated worms. FIG. 8B, Representative figure showing that Gluconoacetobacter feeding does not affect the golgi morphology or distribution as assessed by a transgenic strain that targets GFP to the golgi. FIG. 8C, Representative figure showing that Gluconoacetobacter feeding does not affect the gut lysosomal morphology or distribution as assessed by a transgenic strain that targets GFP to the lysosomes. FIG. 8D, Representative figure showing that Gluconoacetobacter feeding does not affect the Endoplasmic Reticulum (ER) morphology or distribution as assessed by a transgenic strain that targets GFP to the ER. FIG. 8E, Worms fed on Gluconacetobacter spp and treated with H₂O₂ had lower levels of H₂O₂ compared to the worms fed on E. coli OP50 as assessed using the Amplex red assay. FIG. 8F, Glutathione intracellular concentrations were not affected in worms fed on Gluconacetobacter spp compared to worms fed on E. coli OP50. FIG. 8G, Representative figure showing the Halo formation around colonies in CaCO₃ media plates produced by different members of Acetobacteraceae. FIG. 8H, Gluconobacter oxydans transposon mutants failed to suppress the slow developmental growth phenotype of C. elegans spg-7(ad2249).

FIGS. 9A-9E. FIG. 9A, Representative figure showing the Gluconobacter oxydans transposon mutants that failed to suppress the slow developmental growth phenotype of wildtype animals. FIG. 9B, Mutants in membrane-bound PQQ-dependent glucose dehydrogenase, cytochrome o ubiquinol oxidase subunit II, ubiquinol-cytochrome c reductase iron-sulfur subunit, and carbon-nitrogen hydrolase fail to form clear halo around media plates containing CaCO₃. FIG. 9C, Deletion alleles in various dehydrogenases and found that spg-7(ad2249) mutant worms fed on deletion mutations in Membrane-bound PQQ-dependent glucose dehydrogenase, FAD-dependent Membrane-bound dehydrogenase, and Membrane-bound PQQ-dependent dehydrogenase 3 grew slower compared to worms fed on wildtype G. oxydans FIG. 9D, Exposure of E. coli OP50 to human primary dermal fibroblasts results in significant reduction in the ATP production while Gluconacetobacter spp does not affect ATP production compared to the mock-treated cells. FIG. 9E, Gluconacetobacter spp does not reduce the cellular ATP production even at higher doses of the bacteria.

FIGS. 10A-10B. FIG. 10A, Transgenic worms expressing human α-synuclein and GFP in the dopaminergic neurons were fed with E. coli op50 or EBT405 from first larval stage and subjected to Rotenone treatment at the L4-larval stage. Arrows show the axons of CEP neurons. In the rotenone treated animals, the CEP neurons are degenerating or lost. FIG. 10B, Quantification of the CEP neuron loss. Three independent trials were performed and each trial consisted of 20-30 animals.

FIG. 11 Panneuronal expression of human Aβ_(1_42) is sufficient to induce UPR^(mt) reporter phsp-6::gfp in the intestine. Representative fluorescence micrographs of strains either not expressing human Aβ_(1_42) (control strain on the left) and strain expressing the human Aβ_(1_42) (Center and right images) fed on either negative control bacteria or Gluconoacetobacter EBT405 bacteria. All the strains contain phsp-6::gfp and phsp-4::mcherry reporters. While only basal levels of phsp-6::gfp expression is observed in the control strain (Left image), the GFP is activated in the gut of strain carrying human Aβ_(1_42) (Center image); however, in the strain fed on the Gluconoacetobacter EBT405 bacteria, the phsp-6::gfp expression is reduced. The ER unfolded protein response UPR_(ER) reporter phsp-4::mcherry is only weakly activated in the spematheca (white arrowheads). Scale bar on the left image is 200 μM.

FIG. 12 Panneuronal expression of human aggregative tau mutant is sufficient to induce UPRmt stress reporter phsp-6::gfp in the intestine. Representative fluorescence micrographs of strains either not expressing human tau mutant (control strain on the left) and strain expressing the human tau mutant (Center and right images) fed on either negative control bacteria or EBT405 bacteria. All the strains contain phsp-6::gfp, phsp-4::mcherry reporters and a pharyngeal marker (white arrows), pmyo-2:mcherry. While only basal levels of phsp-6::gfp expression is observed in the control strain (Left image), the GFP is activated in the gut of strain carrying human tau mutant (Center image); however, in the strain fed on the Gluconoacetobacter EBT405 bacteria, the phsp-6::gfp expression is reduced. This reduction is specific because the expression of the pharyngeal marker is not affected. The UPRER reporter phsp-4::mcherry is only weakly activated in the spematheca (white arrowheads). Scale bar on the left image is 200 μM.

FIG. 13 shows a schematic representation of the HTS strategy.

FIG. 14 shows data indicating that EBT 405 feeding reduces Aβ aggregates. Representative fluorescence micrographs of CL2331 strain expressing the Aβ₃₋₄₂ peptide conjugated with GFP fed on negative control bacteria or EBT405 and imaged 60 hours post L1 stage. Arrows indicate amyloid deposits. Scale bar, 200 μM

DETAILED DESCRIPTION

Provided herein are methods and compositions for the treatment or prevention of diseases and/or disorders involving or characterized by mitochondrial dysfunction and/or peroxisomal dysfunction. Such compositions comprise one or more bacterial species from the Acetobacteriaceae family or a bacterial extract or component derived therefrom.

Mitochondrial Function/Dysfunction and Production of Intracellular ATP

Mitochondria are intracellular organelles present in most eukaryotic cells, which primarily function to produce energy, in the form of ATP, through oxidative phosphorylation for use in a multitude of cellular processes. For example, energy derived from the metabolism of glucose or fatty acids is converted to ATP, which is then used to drive various energy-requiring biosynthetic reactions and other metabolic activities. Mitochondria have their own genomes, separate from nuclear DNA, comprising circular, double-stranded DNA with about 16,000 base pairs in human cells. Each mitochondrion may have multiple copies of its genome, and individual cells may have hundreds of mitochondria. Mitochondria play a role in the tricarboxylic acid (TCA) cycle, heme synthesis, β-oxidation of fatty acids, amino acid metabolism, and the like. Moreover, functions for maintaining calcium homeostasis, an active oxygen production system, and transport systems for metabolites, ions, proteins, and the like are present in mitochondria. Hence, mitochondria play an important role in both catabolic and anabolic reactions in eukaryotic cells.

It has been shown that mitochondrial dysfunction can contribute to a variety of diseases. Some mitochondrial diseases are due to mutations or deletions in the mitochondrial genome. Mitochondria divide and proliferate with a faster turnover rate than their host cells, and their replication is under control of the nuclear genome. Thus, if a threshold proportion of mitochondria in a cell are defective, and if a threshold proportion of such cells within a tissue have defective mitochondria, symptoms of tissue or organ dysfunction can result. Practically any tissue can be affected, and a large variety of symptoms may be present, depending on the extent to which different tissues are involved.

Diseases of the mitochondria are apparent most often in organs that have a high energy demand, such as the brain, heart, liver, skeletal muscles, kidney and the endocrine and respiratory systems. Even a mild impairment in mitochondrial function can be reflected by symptoms of disease. Symptoms of a mitochondrial disease can include loss of motor control, muscle weakness and pain, seizures, visual/hearing problems, cardiac diseases, liver diseases, gastrointestinal disorders, swallowing difficulties and more. A mitochondrial disease can be inherited or can be due to spontaneous mutations, either of which can lead to altered functions of the proteins or RNA molecules normally residing in the mitochondria.

It is important to note that the bacterial compositions, extracts and/or components described herein will have the greatest effect in cells, tissues, organs, etc. of a subject who retains at least some mitochondrial activity, even if the activity is impaired. While the bacterial compositions, extracts and/or components described herein can induce both mitochondrial and peroxisomal biogenesis (thereby enhancing total cellular metabolic function), the benefit of the compositions described herein is thought to be due to an enhancement of existing mitochondrial function through the electron transport chain. That is, the compositions described herein do not provide an exogenous gene for repair of mitochondrial dysfunction, but rather will enhance the existing function of mitochondria by either increasing the number of mitochondria and/or the function of the electron transport chain within each mitochondrion. This enhancement of function is likely due, in part, to the metabolites generated by the bacteria as described herein.

Disorders associated with impaired mitochondrial function also include, for example, metabolic disorders, neurodegenerative disorders, aging related disorders and chronic inflammatory disorders. Mitochondrial disorders can also include diseases with inherited and/or acquired mitochondrial dysfunction, such as Charcot-Marie-Tooth Disease Type 2A2, Mitochondrial Encephalopathy Lactic Acidosis and Stroke (MELAS), Leigh syndrome, Barth syndrome, Leber's optic neuropathy, fatty acid oxidation disorders, inherited forms of deafness and blindness, metabolic abnormalities induced by exposure to toxic chemicals and/or drugs (e.g., cisplatin induced deafness).

To reiterate, the methods and compositions described herein are not intended to cure diseases or disorders with impaired mitochondrial function but rather are useful in reducing at least one symptom of disease that is associated with impaired mitochondrial function. That is, while the compositions described herein cannot correct an inherited mitochondrial defect, they can be used to enhance mitochondrial function that is present in the cell despite the presence of disease. This can be achieved, for example, by increasing mitochondrial number or increasing flux through the electron transport chain (e.g., at complex I and complex III). Thus, in one embodiment, a subject to be treated with the compositions and methods described herein retains at least 10% mitochondrial and/or peroxisomal function as (prior to treatment) as compared to a non-affected subject. In other embodiments, the subject retains at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% mitochondrial and/or peroxisomal function (prior to treatment) as compared to a non-affected individual.

It is also contemplated herein that individuals who retain normal mitochondrial and/or peroxisomal function can be treated to enhance mitochondrial function to enhance performance, for example, athletic performance.

In certain embodiments, the methods and compositions described herein can increase mitochondrial and/or peroxisomal function by at least 10% (e.g., as assessed by measuring ATP production) compared to the mitochondrial and/or peroxisomal function prior to such treatment. In some embodiments, mitochondrial and/or peroxisomal function is increased by at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, at least 1-fold, at least 2-fold, at least 5-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 1000-fold or more as compared to the mitochondrial and/or peroxisomal function prior to such treatment.

Deficiencies in the Electron Transport Chain:

Many diseases have been found to involve a mitochondrial deficiency such as a Complex I, II, III or IV impairment or an enzyme deficiency e.g. pyruvate dehydrogenase impairment. Complex I, II, III and IV are protein complexes embedded in the inner membrane of the mitochondrion. They are known as the respiratory chain and function by coupling electron transfer between an electron donor (such as NADH) and an electron acceptor (such as 02) with the transfer of H+ ions. The resulting electrochemical proton gradient over the inner membrane is used to generate chemical energy in the form of adenosine triphosphate (ATP) by oxidation of glucose, pyruvate and NADH, which all are produced in the cytosol of the cell. This process of cellular respiration, also known as aerobic respiration, is dependent on the presence of oxygen. When oxygen is limited, the glycolytic products will be metabolized by anaerobic fermentation, a process that is independent of the mitochondria. The production of ATP from glucose is about 13 times higher during aerobic respiration compared to fermentation.

Complexes I-IV carry electrons along four series of reactions, known as the Electron Transport Chain, resulting in energy production. A fifth group (Complex V) is an ATP synthase enzyme that generates ATP. Together, the electron transport chain and the ATP synthase form the respiratory chain and the entire process is known as oxidative phosphorylation or OXPHOS.

Complex I Deficiency:

Complex I, the first step in this chain, is the most common site for mitochondrial abnormalities, representing as much as one third of the respiratory chain deficiencies. Often presenting at birth or in early childhood, Complex I deficiency is usually a progressive neurodegenerative disorder and is responsible for a variety of clinical symptoms, particularly in organs and tissues that require high energy levels, such as brain, heart, liver, and skeletal muscles. A number of specific mitochondrial disorders have been associated with Complex I deficiency including: Leber's hereditary optic neuropathy (LHON), mitochondrial myopathy, encephalopathy, lactic acidosis and stroke (MELAS), myoclonic epilepsy with ragged red fibers (MERRF), and Leigh Syndrome (LS).

To date, three major forms of Complex I deficiency have been identified: i) Fatal infantile multisystem disorder—characterized by poor muscle tone, developmental delay, heart disease, lactic acidosis, and respiratory failure; ii) Myopathy (muscle disease)—starting in childhood or adulthood, and characterized by weakness or exercise intolerance; and iii) Mitochondrial encephalomyopathy (brain and muscle disease)—beginning in childhood or adulthood and involving variable symptom combinations, which can include: eye muscle paralysis, pigmentary retinopathy (retinal color changes with loss of vision), hearing loss, sensory neuropathy (nerve damage involving the sense organs), seizures, dementia, ataxia (abnormal muscle coordination), and involuntary movements. This form of Complex I deficiency may cause Leigh Syndrome and MELAS. Most cases of Complex I deficiency result from autosomal recessive inheritance (combination of defective nuclear genes from both the mother and the father). Less frequently, the disorder is maternally inherited or sporadic and the genetic defect is in the mitochondrial DNA.

In one embodiment, the compositions and methods described herein increase intracellular ATP levels by at least 10%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, at least 1-fold, at least 2-fold, at least 5-fold, at least 10-fold, at least 20 fold, at least 100-fold, at least 1000-fold or more compared to the level of intracellular ATP in a substantially similar cell or cell population, with the exception that the reference cells are not contacted with the compositions or metabolites described herein. In one embodiment, the compositions and methods described herein restore intracellular ATP levels in a subject having mitochondrial dysfunction relative to a subject (or group of subjects) not treated with such compositions and methods.

Metabolic Disorders:

Metabolic disorders include, for example, type II diabetes, obesity, hyperglycemia, glucose intolerance, insulin resistance (i.e., hyperinsulinemia, metabolic syndrome, syndrome X), hypercholesterolemia, hypertension, hyperlipoproteinemia, hyperlipidemia (e.g., dyslipidemia), hypertriglyceridemia, cardiovascular disease, atherosclerosis, peripheral vascular disease, kidney disease, ketoacidosis, thrombotic disorders, nephropathy, diabetic neuropathy, diabetic retinopathy, sexual dysfunction, dermatopathy, dyspepsia, hypoglycemia, metabolic syndrome, cancer or edema. While the methods and compositions described herein may not address the underlying cause(s) of such diseases or disorders, the promotion of mitochondrial function provided by such methods and compositions can ameliorate those aspects of these diseases or disorders that are related to mitochondrial dysfunction or insufficiency.

In one embodiment of the methods and compositions provided herein, the subject is suffering from or is susceptible to developing a metabolic disorder. Subjects suffering from or at risk of developing a metabolic disorder are identified by methods known in the art. For example, diabetes can be diagnosed by measuring e.g., fasting blood glucose levels or insulin or by a glucose tolerance test. Normal adult glucose levels are 60-126 mg/dl. Normal insulin levels are 7 mU/mL±3 mU. Glucose intolerance is diagnosed by a two-hour glucose level of 140 to 199 mg per dL (7.8 to 11.0 mmol) on the 75-g oral glucose tolerance test. Insulin resistance is diagnosed by a fasting serum insulin level of greater than approximately 60 pmol/L. Hypoglycemia can be diagnosed by a blood glucose level lower than 2.8 to 3.0 mmol/L (50 to 54 mg/dl). Hypertension can be diagnosed by a blood pressure consistently at or above 140/90. Cardiovascular disease can be diagnosed, at least in part, by measuring cholesterol levels (e.g., LDL, HDL, VLDL etc.). For example, LDL cholesterol above 137 or total cholesterol above 200 is indicative of cardiovascular disease. Hyperglycemia is diagnosed by a blood glucose level higher than 10 mmol/1 (180 mg/dl). Obesity is diagnosed for example, by body mass index. Alternatively, waist circumference (estimates fat distribution), waist-to-hip ratio (estimates fat distribution), skinfold thickness (if measured at several sites, estimates fat distribution), or bioimpedance (based on principle that lean mass conducts current better than fat mass (i.e., fat mass impedes current), estimates % fat) is measured. The parameters for normal, overweight, or obese individuals are as follows: Underweight: BMI<18.5; Normal: BMI 18.5 to 24.9; Overweight: BMI=25 to 29.9. Overweight individuals are characterized as having a waist circumference of >94 cm for men or >80 cm for women and waist to hip ratios of 0.95 in men and 0.80 in women. Obese individuals are characterized as having a BMI of 30 to 34.9, being greater than 20% above “normal” weight for height, having a body fat percentage >30% for women and 25% for men, and having a waist circumference >102 cm (40 inches) for men or 88 cm (35 inches) for women. Individuals with severe or morbid obesity are characterized as having a BMI of

Neurodegenerative Disease:

Neurodegenerative disorders include diseases such as dementia, Alzheimer's disease, Parkinson's disease, and Huntington's disease.

In one embodiment, the neurodegenerative disorder is Parkinson's disease. Parkinson's disease (PD) is a neurodegenerative movement disorder characterized by resting tremor, rigidity, bradykinesia, and postural instability. PD symptoms are classically attributed to dopamine depletion and the degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNc). However, additional neuronal circuits are affected, and non-motor symptoms are often present, suggesting a systemic pathology. There is compelling evidence that mitochondrial dysfunction is a primary event in the disease process. It has been reported that PD-related mutations and mitochondrial dynamics have a reciprocal relationship. PD-related mutations can perturb mitochondrial dynamics, and the consequences of these mutations can be modulated by mitochondrial dynamics.

In one embodiment, effective treatment of Parkinson's disease is determined by a reduction in the dose of pharmacological treatments, such as L-DOPA, required to maintain adequate control of symptoms of Parkinson's disease. In another embodiment, efficacy of treatment is monitored using the Unified Parkinson's Disease Rating Scale (UPDRS) as known in the art.

Alzheimer's disease, amyotrophic lateral sclerosis (ALS), Huntington's disease, Friedrich's ataxia, hereditary spastic paraplegia, neurodegeneration with brain iron accumulation (NBIA), and optic atrophy type I are also each associated with various mitochondrial activity deficits (see e.g., Lin et al. Nature 443: 787-795 (2006)).

Inflammatory Disease:

Chronic inflammatory diseases include disease such as celiac disease, vasculitis, lupus, chronic obstructive pulmonary disease (COPD), irritable bowel disease, atherosclerosis, arthritis, and psoriasis. While the methods and compositions described herein may not address the underlying cause(s) of such diseases or disorders, the promotion of mitochondrial function provided by such methods and compositions can ameliorate those aspects of these diseases or disorders that are related to mitochondrial dysfunction or insufficiency.

Aging:

Aging is a progressive accumulation of metabolic and physiologic changes associated with an increasing susceptibility to disease. In the membrane hypothesis of aging (MHA), aging is related to decreasing effectiveness of cellular protective and reparative mechanisms secondary to damage from oxygen radicals. This yields biochemical and metabolic errors which progressively accumulate, resulting in cell aging and ultimately death. Therefore, the MHA suggests that reactive oxygen species (ROS) induced cell membrane structural damage is the primary mediator in cellular aging.

ROS are a normal byproduct of oxidative phosphorylation, and are also formed under conditions of ischemia, hypoperfusion and in response to environmental contaminants. Among the many detrimental activities of ROS, or free oxygen radicals, is direct damage to mitochondrial DNA (mtDNA). Progressive accumulation of mtDNA damage renders cells unable to conduct oxidative phosphorylation reactions effectively, thereby leading to a bioenergetically deficient cell. Over time, mitochondrial DNA damage accumulates and leads to cellular dysfunction with subsequent organ failure, aging and ultimately death. Additionally, there is evidence of a reduction in the oxidant-protective enzymes superoxide dismutase and catalase associated with aging. Thus not only are there increases in the deleterious effects of ROS, but there is a reduction in the enzymes and mitochondrial metabolites necessary for protection from ROS and for effective mitochondrial function.

Peroxisomal Disorders

In some embodiments, the subject has a peroxisomal disorder, with or without the presence of mitochondrial dysfunction.

Peroxisomes are intracellular organelles that are expressed in all eukaryotic cells except erythrocytes and play an important role in intracellular metabolism. Peroxisomes are dynamic organelles that change in shape and numbers based on the specific metabolic needs of different tissues and cell types. Peroxisomes are capable of catabolizing very long chain fatty acids to shorter fatty acids that can then enter the B-oxidation cycle. (VLCFA: carbon chain >22). Peroxisomes also play a role in intracellular antioxidant activity.

Peroxisomes are also involved in the synthesis of lipids such as bile acids, docosohexanoic acid, an omega 3 fatty acid, and plasmalogens, a specialized class of membrane phospholipids. Although a single cell may be able to survive without peroxisomes in certain conditions, this organelle is essential for the proper function and viability of tissues and organs. The importance of peroxisomes is most evident by the group of diseases resulting from the lack of functioning peroxisomes called Peroxisome Biogenesis Disorders or “PBD” (Weller et al., 2003).

In some embodiments, the methods and compositions described herein are not intended to cure peroxisomal diseases or disorders but rather are useful in reducing at least one symptom of disease that is associated with impaired peroxisomal function. That is, while the compositions described herein cannot correct an inherited peroxisomal defect, they can be used to enhance existing peroxisomal function. This can be achieved, for example, by increasing peroxisomal number or increasing flux through the metabolic pathways of the peroxisome (e.g., metabolism of very long chain fatty acids (VLCFA). Thus, in one embodiment, a subject to be treated with the compositions and methods described herein retains at least 10% of the peroxisomal function as compared to the peroxisomal function of a non-affected subject. In other embodiments, the subject retains at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% peroxisomal function as compared to a non-affected individual.

Peroxisome Biogenesis Disorders are a continuum of disorders that are divided into three phenotypes based on the severity of the disorder. Zellweger Syndrome (ZS) is the most severe form; followed by neonatal adrenoleukodystrophy (NALD), an intermediate form, and infantile Refsum disease (IRD), which is the least severe. Children with ZS present early in the neonatal period with profound hypotonia, facial dysmorphisms, liver dysfunction, seizures, and rarely survive past their first year of life. At a biochemical level, laboratory tests show profound deficiencies in peroxisomal metabolism and cells from these patients show near absence of functional cellular peroxisomes. NALD and IRD are more difficult to distinguish from each other, form the majority of cases, and patients can live through adulthood. Both may present soon after birth, but are often diagnosed later by developmental delays, mild liver dysfunction, and hearing and visual impairment leading to their classification as deaf-blind children. A proportion of NALD-IRD children will develop a leukodystrophy that represents destruction of normal myelin. They may also develop adrenal gland insufficiency and osteopenia, the latter causing pathological fractures. Cells from patients with NALD-IRD contain more functional peroxisomes than ZS patients, and laboratory tests show higher residual peroxisome metabolism. Clinical features result from deficiency of products made by the peroxisome and toxicity of substrates that accumulate (such as very long chain fatty acids).

These autosomal recessive diseases are derived from dysfunction of peroxisomes and current treatment is primarily focused on supportive care, dietary management, symptomatic therapy and treatment strategies involving the use of pharmacological induction of peroxisomes. Administration of bacteria, or an extract or metabolite preparation, as described herein to a subject with a peroxisome deficiency can improve peroxisome activities or function and thereby provide therapeutic benefit.

Engineered Bacteria

In some embodiments, one or more of the compositions or bacterial extracts as described herein comprises an engineered microbe(s). For example, engineered microbes include microbes harboring one or more introduced genetic changes, such change being an insertion, deletion, translocation, or substitution, or any combination thereof, of one or more nucleotides contained on the bacterial chromosome or on an endogenous plasmid, wherein the genetic change can result in the alteration, disruption, removal, or addition of one or more protein coding genes, non-protein-coding genes, gene regulatory regions, or any combination thereof, and wherein such change can be a fusion of two or more separate genomic regions or can be synthetically derived. The engineered microbe(s) can be produced using techniques including but not limited to site-directed mutagenesis, transposon mutagenesis, knock-outs, knock-ins, polymerase chain reaction mutagenesis, chemical mutagenesis, ultraviolet light mutagenesis, transformation (chemically or by electroporation), phage transduction, or any combination thereof.

In one embodiment, the bacterium is from the Acetobacteriaceae family of gram negative bacteria. Members of the Acetobacteriaceae family are generally grouped according to their ability to oxidize sugars or ethanol to produce acetic acid during fermentation. In one embodiment, the bacterium is an Acetobacter spp., which is distinguished from other members of the Acetobacteriaceae family, including Gluconobacter spp., and Gluconoacaetobacter spp.

In another embodiment, the bacterium is a Gluconobacter spp. Non-limiting examples of Gluconobacter spp. include Gluconobacter albidus, Gluconobacter asaii, Gluconobacter cerevisiae, Gluconobacter cerinus, Gluconobacter frateruii, Gluconobacter japonicus, Gluconobacter kanchanaburiensis, Gluconobacter kondonii, Gluconobacter nephelii, Gluconobacter oxydans, Gluconobacter sphaericus, Gluconobacter thailandicus, Gluconobacter uchimurae, and Gluconobacter wancherniae.

In another embodiment, the bacterium is a Gluconacetobacter spp. Non-limiting examples of Gluconacetobacter spp. include Gluconoacaetobacter aggeris, Gluconoacaetobacter asukensis, Gluconoacaetobacter azotocaptans, Gluconoacaetobacter diazotrophicus, Gluconoacaetobacter entanii, Gluconoacaetobacter europaeus, Gluconoacaetobacter hansenii, Gluconoacaetobacter intermedius, Gluconoacaetobacter johannae, Gluconoacaetobacter kakiaceti, Gluconoacaetobacter kombuchae, Gluconoacaetobacter liquefaciens, Gluconoacaetobacter maltaceti, Gluconoacaetobacter medellinensis, Gluconoacaetobacter nataicola, Gluconoacaetobacter oboediens, Gluconoacaetobacter rhaeticus, Gluconoacaetobacter sacchari, Gluconoacaetobacter saccharivorans, Gluconoacaetobacter sucrofermentans, Gluconoacaetobacter swingsii, Gluconoacaetobacter takamatsuzukensis, Gluconoacaetobacter tumulicola, Gluconoacaetobacter tumulisoli, and Gluconoacaetobacter xylinus. In another embodiment of this aspect and all other aspects provided herein, the bacterium is Gluconobacter EBT 405.

In some embodiments, the bacterium is Gluconobacter albidus, Gluconobacter cerinus, Gluconobacter frateruii, Gluconobacter japonicus, Gluconobacter kondonii, Gluconobacter nephelii, Gluconobacter oxydans, Gluconoacetobacter diazotrophicus, Gluconoacetobacter hansenii, Gluconoacetobacter saccharivorans, Acetobacter aceti or Acetobacter malorum.

In some embodiments, the bacterium is not a member of the Acetobacteriaceae family but is genetically modified to produce similar metabolites (e.g., gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid). For example, in some embodiments, a bacterium as described herein is genetically modified to express, e.g., one or more of: membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II. Methods of introducing heterologous genetic material to bacterial cells by transformation or transduction are well known, and include, as non-limiting examples, chemical transformation, particle bombardment, and electroporation. The approach best suited to a given bacterium will be known to those of ordinary skill in the art.

The following sequences are provided for selected metabolic pathway enzymes that can be expressed in an engineered bacterium.

SEQ ID NO: 1 >mGDH nucleotide sequence atgagcacaatttcccggccagggctctgggccctgataacggccgcggtattcgcgctttgcggcgc gatccttaccgttggcggcgcatgggtcgctgccatcggcggccctctttattatgtcatccttggcc tggcacttctcgccacggctttcctctcattccggcgcaatccggctgccctctatctgttcgcagtc gtcgtcttcggaacggtcatctgggaactcaccgttgtcggtctcgacatctgggccctgatcccgcg ctcggacatcgtcatcatcctcggcatctggctgctgctgccgttcgtctcgcgccagatcggtggca cgcggacgaccgtcctgccgctcgccggcgccgttggcgttgcggttctggccctgttcgccagcctc ttcaccgacccgcatgacatcagcggcgaactgccgacgcagatcgcaaacgcctcccccgccgaccc ggacaacgttccggccagcgagtggcacgcttatggtcgtacgcaggccggtgaccgctggtccccgc tgaaccagatcaatgcgacgaacgtcagcaacctcaaggtcgcatggcatatccacaccaaggatatg atgaactccaacgacccgggcgaagcgacgaacgaagcgacgccgatcgagttcaacaacacgcttta tatgtgctcactgcatcagaagctgtttgcggttgatggtgccaccggcaacgtcaagtgggtctacg atccgaagctccagatcaaccctggcttccagcatctgacctgccgtggcgtcagcttccacgaaacg ccggccaatgccatggattccgatggcaatcctgctccgacggactgcgccaagcgcatcatcctgcc ggtcaatgatggccgtctggttgaagtcgatgccgacacgggcaagacctgctccggcttcggcaaca atggcgagatcgacctgcgcgttccgaaccagccttacacgacgcctggccagtacgagccgacgtcc ccgccggtcatcacagacaagctgatcatcgccaacagcgccatcaccgataacggttcggtcaagca ggcttcgggcgccacgcaggcattcgacgtctacaccggcaagcgcgtctgggtgttcgatgcgtcca acccggatccgaaccagcttccggatgagagccaccctgtcttccacccgaactcgccaaactcctgg atcgtgtcgtcctacgacgccaacctgaacctcgtgtacatcccgatgggcgtggggactcccgacca gtggggcggtgaccgcacgaaggattccgagcgtttcgctccgggtatcgttgcgctgaacgccgata cgggcaagctcgcctggttctaccagaccgttcatcacgatctgtgggacatggacgttccgtcccag ccgagcctcgtggatgtgacacagaaggacggcacgcttgttccggccatctacgctccgaccaagac cggcgacattttcgtcctcgaccgtcgtaccggcaaggaaatcgtcccggctccggaaaccccggttc cccagggtgctgctccgggtgaccacaccagcccgacccagccgatgtcgcagctgaccctgcgtccg aagaacccgctgaacgactccgatatctggggcggcacgatcttcgaccagatgttctgcagcatcta tttccacaccctccgctacgaaggccccttcacgccgccgtcgctcaagggctcgctcatcttcccgg gtgatctgggaatgttcgaatggggtggtctggccgtcgatccgcagcgtcaggtggctttcgccaac ccgatttccctgccgttcgtctctcagcttgttccccgcggaccgggcaacccgctctggcctgaagg aaatgccaagggcacgggtggtgaaaccggcctgcagcacaactatggcatcccgtatgccgtcaacc tgcatccgttcctggatccggtgctgctgccgttcggcatcaagatgccgtgccgcacgccgccctgg ggctatgtcgccggtattgacctgaagaccaacaaggtcgtctggcagcaccgcaacggcaccctgcg tgactcgatgtatggcagctccctgccgatcccgctgccgccgatcaagatcggtgtcccgagcctcg gtggcccgctctccacggctggcaatctcggcttcctgacggcgtccatggattactacatccgtgcg tacaacctgacgacgggcaaggtgctgtggcaggaccgtctgccggctggtgctcaggcaacgccgat cacctatgccatcaacggcaagcagtacatcgtgacctatgcaggcggacacaactcgttcccgaccc gcatgggcgacgacatcatcgcctacgccctgcccgatcagaaatga SEQ ID NO: 2 >mGDH protein sequence MSTISRPGLWALITAAVFALCGAILTVGGAWVAAIGGPLYYVIL GLALLATAFLSFRRNPAALYLFAVVVFGTVIWELTVVGLDIWALIPRSDIVIILGIWL LLPFVSRQIGGTRTTVLPLAGAVGVAVLALFASLFTDPHDISGELPTQIANASPADPD NVPASEWHAYGRTQAGDRWSPLNQINATNVSNLKVAWHIHTKDMMNSNDPGEATNEAT PIEFNNTLYMCSLHQKLFAVDGATGNVKWVYDPKLQINPGFQHLTCRGVSFHETPANA MDSDGNPAPTDCAKRIILPVNDGRLVEVDADTGKTCSGFGNNGEIDLRVPNQPYTTPG QYEPTSPPVITDKLIIANSAITDNGSVKQASGATQAFDVYTGKRVWVFDASNPDPNQL PDESHPVFHPNSPNSWIVSSYDANLNLVYIPMGVGTPDQWGGDRTKDSERFAPGIVAL NADTGKLAWFYQTVHHDLWDMDVPSQPSLVDVTQKDGTLVPAIYAPTKTGDIFVLDRR TGKEIVPAPETPVPQGAAPGDHTSPTQPMSQLTLRPKNPLNDSDIWGGTIFDQMFCSI YFHTLRYEGPFTPPSLKGSLIFPGDLGMFEWGGLAVDPQRQVAFANPISLPFVSQLVP RGPGNPLWPEGNAKGTGGETGLQHNYGIPYAVNLHPFLDPVLLPFGIKMPCRTPPWGY VAGIDLKTNKVVWQHRNGTLRDSMYGSSLPIPLPPIKIGVPSLGGPLSTAGNLGFLTA SMDYYIRAYNLTTGKVLWQDRLPAGAQATPITYAINGKQYIVTYAGGHNSFPTRMGDD IIAYALPDQK SEQ ID NO: 3 >ubiquinol-cytochrome c reductase iron-sulfur subunit nucleotide sequence atgacccaggacgatgcctctctcatttctgatccaacgtcttccagacaggaggaggggtctcgccg cagggatgtgctggcaacggtaacagttgccatgggatgtgcaggcgcgtgtgctgtggcctatcctt ttctggacagcctgaatgggacgcgcgccaatcatgtcggggagagcgacatcctggacgtggatctc tctaccctcaaagccggccagcagattgttgtgacatggcgggggtggcccgtgttcgtgcagagaag aacgccagaaatgctgaaaacgcttcaggatccggcaatcctgcagaaactacgagatcctgagtcct gcattttccaacaacccaaagacgcaacaaactggcatcgttccgtcagccccgatatcggcgtcatg attgggatctgtacccatctcggctgcgtgccgactttcgacgccccgacgcaggcagaacctgccgg gaaatacctctgcccctgtcatggttcacagtttgacagtgcaggccgcgcctacaggaacgcccctg caccatacaatctgccggttccgcccgtgacaatgatttccgatacgcatctgcgaattggagaaagc aaaaacgatcctgactttgatattgctaacatccagcagatctga SEQ ID NO: 4 >ubiquinol-cytochrome c reductase iron-sulfur subunit protein sequence MTQDDASLISDPTSSRQEEGSRRRDVLATVTVAMGCAGACAVAY PFLDSLNGTRANHVGESDILDVDLSTLKAGQQIVVTWRGWPVFVQRRTPEMLKTLQDP AILQKLRDPESCIFQQPKDATNWHRSVSPDIGVMIGICTHLGCVPTFDAPTQAEPAGK YLCPCHGSQFDSAGRAYRNAPAPYNLPVPPVTMISDTHLRIGESKNDPDFDIANIQQI SEQ ID NO: 5 >TonB-dependent receptor nucleotide sequence atgatcgtatcgcgtcgcaatacgttactttgcgcatcggtgctggggatgggggcgctttcgagcgt tgctcatgcggcaaccgaaagcactcacacgtcctcacatgtgcgccacaagactgtgactcatggtc cggtgcgttctgctgcgacgcctgcaacaacagctccggtctcggtagctcgtccggtggcagctccg cagttttctgcacctgtagcggtcaaccggtcccatgccgttcgttccattgattccggaacgcagga aagcgttgtggtcacggggtcggctctgagcacgtctaacaatcagaacgcgaacccggtccagatcg tgaccagcaagcagatcgagcagactggcatcaacactctgggtgattacctgcagcgcctgccgtct gtcggttcttcgggtacgacgaacagccaaaccaacaatacggcgggtgtttcttgcacggatatccg taaccttggcaaaagccgtgttctggttctgattgatggcaagcgtgcagcaattgacggctcgtcaa gctgctttgatctgaacaccatcaatattcaccaggtggcgagtgtcgaaatcctcaaggatggtggt tctgagctgtatggtgctgatgccgtttccggtgtcatcaacatcaagctcaaacacaatctggatga cgcgaacctgacggttcgtggaggcatcactgaccgtggagatggccagtccggcatgatttctggct acaagggctggaattttgatcatggccgcggcaacgtgacggtctccggatcttacatgacccagagc gggatccgtcagaacagccgtgactgggccaacccggttgtgtctggtctgattgcaccgggtggttc gccgacttacggatcgtccatcccgacggcgggtcgtttcatcactgatactgcggataatgttccca atggtgatggatcgttccacaatttcagcaagaaagatcgctacaactacggtaatgatcagagcctg acgaactccttgcaggatgccacgctgtcgttcgatgcacattacgacgtgaaccgtcatttcacgcc gtatggcaacttcctgtattcgcatcgtaactctaatacgcagatggcgccgattccggtgtctggta gcatctacccgtccactctgccggtagccatcaccattccaggaagtgcgccgtacaattcgcttggc gaagatgccacgatgtacaagcgtatgggtgaatggggtgatcgcgtcagtcagactgctaccgacac atacacggcaaagattggcgcttcgggtgatatcacccacggttggaaatatgacctgtcctatacct acggatggaaccaggtcatgtcccagacttctggcgttggtaattattccaagctgcttcagagctac ggtctatccgctgaagagccgggcaatcctgacagtgcgctggtttacaacccgtcgatctgcactgc agcggctggctgcacactgtccaaccctttcaacaagctttcgccgcaagcggctgattactcgaact acacgtcgcacgatcactactactatcagctgcgtgatctgaacctgcgtattaacaataaccatgtt gttcacatgccgtggaagaacggtggcgatctaggtatcgcgctgggtatggagcatcgtggtgagca gcttgcctatcatccggatgccctcgttgaatctggccagacgctgacgaactctgcttcctacacgg gtggtggattcaacgtcacggaaggctacctcgaaggtaaagccacgctgctgcacaatgcattcctt gccaaggatctgacgattgacggtcagggccgttactcgtcttacaacacgttcggcagcacgaagaa ctggaaggcgtccatcaactgggcaccggttcaggacatccgcttccgtgcaacgcttggcacgtcct accgtcagcctaacgtctatgagctgtatggcggtcagtctctcggctatgcatcagcaactgaccca tgcgacagcgggcaggtcggcacatatggcagtctgacgccaattgtggcggcaaattgcgccaagca ggggattaacagcagtaatttcgtgtctgcttcctccagtcaggttccgaccctgtttggtggcaatc ccaagctgaagcctgaaactggccgtacctacacgtttggtacaacggtcacgccgcgttggattcca ggcctctcggcttccgtggaatactggcattacacgctcaagaacatgatttcgtacctgagcagtca gtacatcatgaaccagtgctacacgggtgcaaacacgtcatattgcaatgacattacccgcgttggca gcacgaaccagctaaactccgtgacagctctgtatggcaacatcggcggactgaagacgagcggcatc gactttgaccttgactaccgtatccgcgttacatctcgcgacgttctgacattgtccaacaactttca gcaacttgtgagctatcttcagcagaacgagctcggcggaaagtggtacaattatgcaggtcgcatgt tctaccaaaacggtactggcaacccccgcgttcgtgattatgcgaccgttggctggcagcatggtgca attggcgtcacatatatgatgagctatatgggtggtatgcgttggaacgactcggaaactgatgtgac ccgttcagcttcgggccgcatcaagacgcctggcatcttctctcatgatgttacggtgacttatcgtt ggaaaaagtggaacttcgaagctggtgtgaacaacctgctcgacaagaagcctccctttgtttctggt gggacagacaacagcgcggctgccctttatggcaacctttacatgggacgtaacgtcttcctgcaggc aggcgtgaacttctga SEQ ID NO: 6 >TonB-dependent receptor protein sequence MIVSRRNTLLCASVLGMGALSSVAHAATESTHTSSHVRHKTVTH GPVRSAATPATTAPVSVARPVAAPQFSAPVAVNRSHAVRSIDSGTQESVVVTGSALST SNNQNANPVQIVTSKQIEQTGINTLGDYLQRLPSVGSSGTTNSQTNNTAGVSCTDIRN LGKSRVLVLIDGKRAAIDGSSSCFDLNTINIHQVASVEILKDGGSELYGADAVSGVIN IKLKHNLDDANLTVRGGITDRGDGQSGMISGYKGWNFDHGRGNVTVSGSYMTQSGIRQ NSRDWANPVVSGLIAPGGSPTYGSSIPTAGRFITDTADNVPNGDGSFHNFSKKDRYNY GNDQSLTNSLQDATLSFDAHYDVNRHFTPYGNFLYSHRNSNTQMAPIPVSGSIYPSTL PVAITIPGSAPYNSLGEDATMYKRMGEWGDRVSQTATDTYTAKIGASGDITHGWKYDL SYTYGWNQVMSQTSGVGNYSKLLQSYGLSAEEPGNPDSALVYNPSICTAAAGCTLSNP FNKLSPQAADYSNYTSHDHYYYQLRDLNLRINNNHVVHMPWKNGGDLGIALGMEHRGE QLAYHPDALVESGQTLINSASYTGGGFNVTEGYLEGKATLLHNAFLAKDLTIDGQGRY SSYNTFGSTKNWKASINWAPVQDIRFRATLGTSYRQPNVYELYGGQSLGYASATDPCD SGQVGTYGSLTPIVAANCAKQGINSSNFVSASSSQVPTLFGGNPKLKPETGRTYTFGT TVTPRWIPGLSASVEYWHYTLKNMISYLSSQYIMNQCYTGANTSYCNDITRVGSTNQL NSVTALYGNIGGLKTSGIDFDLDYRIRVTSRDVLTLSNNFQQLVSYLQQNELGGKWYN YAGRMFYQNGTGNPRVRDYATVGWQHGAIGVTYMMSYMGGMRWNDSETDVTRSASGRI KTPGIFSHDVIVTYRWKKWNFEAGVNNLLDKKPPFVSGGTDNSAAALYGNLYMGRNVF LQAGVNF SEQ ID NO: 7 >carbon-nitrogen hydrolase nucleotide sequence atgcgcgttgccctgatccagatggctccttcggcggaccggagtgccaatatccttcaagctcagcg gctggtttcagaagctgtcaaagctcggaagccagatcttgtggtgctgcctgaaatctggagctgtc tgggtggttcggctgcgaccaagcaggctaatgcagagcttctacctgatccaggcgatgctggaggt gtactctacgaagcgttgagggccatggcccgggaacataatgtctgggttcacggtggttcaatcgg agaacttgtagggcctgagtcgggcgacaagcttgccaatacttcactcgttttcaaccctgatggcg aggaatgtgggcgttacagaaaaatccatctcttcgatgttattacacccaatggggacggctatcgt gaaagcgataattatgtgcccggggaagcgatcgaagtcgtcgatattgatggcgtcccaaccggcct cgcgatttgctatgatttgaggtttgctgagctgtttcttgcacttcgggctgcggatgttgagatga ttgttctgcccgcagcgtttacgcagcaaacgggtgaagctcactgggacattcttgtccgtgctcgc gctattgagtctcagacgtgggtgatagcgtgtggaacaacgggctggcatgtcgatgggcaaggcaa tcagcgccagacctatggccattccatgatcgtcagcccatggggcgaggttgttcttcaattgggta gtgaagaaggctggggggtggctgatcttgatatggatgaggttcgacaggtgcgggagagaatgcct gtgcagataaacaggcggctgatttga SEQ ID NO: 8 >carbon-nitrogen hydrolase protein sequence MRVALIQMAPSADRSANILQAQRLVSEAVKARKPDLVVLPEIWS CLGGSAATKQANAELLPDPGDAGGVLYEALRAMAREHNVWVHGGSIGELVGPESGDKL ANTSLVFNPDGEECGRYRKIHLFDVITPNGDGYRESDNYVPGEAIEVVDIDGVPTGLA ICYDLRFAELFLALRAADVEMIVLPAAFTQQTGEAHWDILVRARAIESQTWVIACGTT GWHVDGQGNQRQTYGHSMIVSPWGEVVLQLGSEEGWGVADLDMDEVRQVRERMPVQIN RRLI SEQ ID NO: 9 >ubiquinol oxidase subunit II nucleotide sequence atgatgaaagcaggaccgatgaaaaaactctggcgatatctcccagcgttgccggcgctgatgctatc gggttgcacggttgatctgcttcagccgcgcggtccgatcgcagaaatgaaccgcgacgttatggtgg cagaatttgccatcatgatggcgattgtggttccgacctgtatcgcaacgctttattttgcttggaag tatcgcgcttccaatacccaggccgaatatctgccgacctgggatcactcaacgaagattgagtatgt catctggggcgtccctgctctgatcattattgcccttggcgcgatcagctggtacagcacccatgctt atgacccgtaccgcccgctccagacggctgacaacgtcaagccgctgaacgttcaggtggtctctctc gactggaaatggctgttcatctatccggatctggggatcgccacgatcaaccagctggatgtgcccac gaacacgccgctgaacttccagatcacctctgacactgtcatgacgtcgttcttcatcccgcgtctgg gatcaatgatctactccatgccgggtcagcagacacagctgcatcttcttgcaactgagtcgggtgac tatctgggtgaagcttcccagttcagtggtcgcggtttctctgacatgaagttccgcaccctcgccat ggcacctgaagaattcagcgcctgggtcgagaaggtgaagagcggcagcgaaaacctcgatgacacga cttatccgaagtacgccgccccgcaggaagctgcgccggttcagtatttcgcgcatgtccagccggat ctcttcgacggcatcgtcgccaagtacaacaatggcatgatggttgagaagacgacgggcaaggtcat gcatatgcagtccgcttccagcgctgcaccgtccgacactggcatgaaggaataa SEQ ID NO: 10 >ubiquinol oxidase subunit II protein sequence MMKAGPMKKLWRYLPALPALMLSGCTVDLLQPRGPIAEMNRDVM VAEFAIMMAIVVPTCIATLYFAWKYRASNTQAEYLPTWDHSTKIEYVIWGVPALIIIA LGAISWYSTHAYDPYRPLQTADNVKPLNVQVVSLDWKWLFIYPDLGIATINQLDVPTN TPLNFQITSDTVMTSFFIPRLGSMIYSMPGQQTQLHLLATESGDYLGEASQFSGRGFS DMKFRTLAMAPEEFSAWVEKVKSGSENLDDTTYPKYAAPQEAAPVQYFAHVQPDLFDG IVAKYNNGMMVEKTTGKVMHMQSASSAAPSDTGMKE

In order to facilitate transfer of genetic material (e.g., a plasmid, DNA etc.) to a bacterium, artificial cell competence can be induced by exposing the bacterium to particular conditions. For example, one method of inducing cell competence is by incubating the bacterium in a solution with divalent cations (e.g., calcium chloride) to partially disrupt the membrane and then heat-shocking the host cells to induce them to take up e.g., plasmid DNA. An alternative method for inducing cell competence is electroporation, where the cells are exposed to an electric field, which can generate small holes in the cell membrane such that plasmid DNA can enter the cell.

The plasmid-supplied nucleic acid (e.g., DNA) can be stably integrated into the genome or can be maintained episomally, e.g., on a plasmid or other episomal vector. In some embodiments, a sequence directing the expression of the one or more enzymes described herein can be placed under the control of naturally-occurring regulatory elements in the cell. In other embodiments, constructs for the expression of at least one of: membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II will generally include regulatory elements, including, promoters, enhancers, etc. that direct the expression of the encoded sequences. A gene under the control of a set of regulatory elements is generally referred to as “operably linked” to those elements. Typically, an expression vector comprises a transcription promoter, a transgene encoding sequence, and a transcription terminator.

An expression vector, or a vector, as described herein, is a nucleic acid molecule encoding a gene that is expressed when the molecule is introduced to a host-cell. Typically, an expression vector comprises a transcription promoter, a gene encoding sequence, and a transcription terminator. Gene expression in an expression vector is usually placed under the control of a promoter, and such a gene is said to be “operably linked to” the promoter. Similarly, a regulatory element and a core promoter are operably linked if the regulatory element modulates the activity of the core promoter.

In some embodiments it may be useful to include in the transformed cells a positive marker that permits the selection of cells positive for the plasmid-supplied nucleic acid sequence(s) in vitro. The positive selectable marker may be a gene that upon being introduced into the host cell expresses a dominant phenotype permitting positive selection of cells carrying the gene. Genes of this type are known in the art, and include, for example, an antibiotic resistance gene (e.g., resistance to blasticidin, mycophenolic acid, puromycin, zeocin, actinomycin, ampicillin, kanamycin, neomycin, polymixin B sulfate, or streptomycin), or an enzyme that converts a substrate to a colored product (e.g., blue/white screening by expression of B-galactosidase, which converts X-gal into galactose and an insoluble blue pigment) etc. Other selection tools can include e.g., radioactive nucleic acid probes, and labeled antibodies that are specific to the protein expressed by the transgene.

Prebiotics

A prebiotic is an ingredient or compositions that is not digestible by a bacterial host, e.g., a h human, but that is fermentable by, and selectively promotes the growth and/or activity of beneficial bacteria in the host. Such selective fermentation that allows specific changes, both in the composition and/or activity of the gastrointestinal microbiota, that confers neutral or positive benefits upon host well-being and health. Prebiotics can include complex carbohydrates, amino acids, peptides, or other nutritional components useful for the survival, colonization and persistence of the bacterial composition.

Suitable prebiotics are usually plant-derived complex carbohydrates, oligosaccharides or polysaccharides. Generally, prebiotics are indigestible or poorly digested by humans and serve as a food source for bacteria. Prebiotics, which can be used in the pharmaceutical dosage forms, and pharmaceutical compositions and methods provided herein include, without limitation, galactooligosaccharides (GOS), trans-galactooligosaccharides, fructooligosaccharides, or oligofructose (FOS), inulin, oligofructose-enriched inulin, lactulose, arabinoxylan, xylooligosaccharides (XOS), mannooligosaccharides, gum guar, gum Arabic, tagatose, amylose, amylopectic, xylan, pectin, combinations thereof, and the like.

In some embodiments, the prebiotic comprises a mixture of one or more non-digestible oligosaccharides, non-digestible polysaccharides, free monosaccharides, non-digestible saccharides, starch, or non-starch polysaccharides. Suitable oligosaccharides and their production methods are further described in Laere K J M, “Degradation of structurally different non-digestible oligosaccharides by intestinal bacteria: glycosylhydrolases of Bi. Adolescentis (2000) PhD thesis, Wageningen Agricultural University, Wageneingen, The Netherlands.

Culture and Storage of Bacteria

For banking, the strain(s) included in the bacterial composition can be (1) isolated directly from a specimen or taken from a banked stock, (2) optionally cultured on a nutrient agar or broth that supports growth to generate viable biomass, and (3) the biomass optionally preserved in multiple aliquots in long-term storage.

In embodiments using a culturing step, the agar or broth contains nutrients that provide essential elements and specific factors that enable growth. An example would be a medium composed of 20 g/L glucose, 10 g/L yeast extract, 10 g/L soy peptone, 2 g/L citric acid, 1.5 g/L sodium phosphate monobasic, 100 mg/L ferric ammonium citrate, 80 mg/L magnesium sulfate, 10 mg/L hemin chloride, 2 mg/L calcium chloride, and 1 mg/L menadione. A variety of microbiological media and variations are well known in the art (e.g. R. M. Atlas, Handbook of Microbiological Media (2010) CRC Press). Medium can be added to the culture at the start, can be added during the culture, or can be intermittently/continuously flowed through the culture. The strains in the bacterial composition can be cultivated alone, as a subset population of a bacterial composition, or as an entire population of different species or strains comprising a bacterial composition. As an example, a first strain can be cultivated together with a second strain in a mixed continuous culture, at a dilution rate lower than the maximum growth rate of either cell to prevent the culture from washing out of the cultivation.

The inoculated culture is incubated under favorable conditions for a time sufficient to build biomass. For bacterial compositions for human use this is often at normal body temperature (37° C.), pH, and other parameter with values similar to the normal human niche. The environment can be actively controlled, passively controlled (e.g., via buffers), or allowed to drift. For example, for anaerobic bacterial compositions (e.g., gut microbiota), an anoxic/reducing environment can be employed. This can be accomplished by addition of reducing agents/factors such as cysteine to the broth, and/or stripping it of oxygen. As an example, a culture of a bacterial composition can be grown at 37° C., pH 7, in the medium above, pre-reduced with 1 g/L cysteine.HCl.

When the culture has generated sufficient biomass, it can be preserved for banking or storage. The organisms can be placed into a chemical milieu that protects from freezing (adding ‘cryoprotectants’), drying (‘lyoprotectants’), and/or osmotic shock (‘osmoprotectants’), dispensing into multiple (optionally identical) containers to create a uniform bank, and then treating the culture for preservation. Containers are generally impermeable and have closures that assure isolation from the environment. Cryopreservation treatment is accomplished by freezing a liquid at ultra-low temperatures (e.g., at or below −80° C.). Dried preservation removes water from the culture by evaporation (in the case of spray drying or ‘cool drying’) or by sublimation (e.g., for freeze drying, spray freeze drying). Removal of water improves long-term bacterial composition storage stability at temperatures elevated above cryogenic. If the bacterial composition comprises spore forming species and results in the production of spores, the final composition can be purified by additional means such as density gradient centrifugation and preserved using the techniques described above. Bacterial composition banking can be done by culturing and preserving the strains individually, or by mixing the strains together to create a combined bank. As an example of cryopreservation, a bacterial composition culture can be harvested by centrifugation to pellet the cells from the culture medium, the supernatant decanted and replaced with fresh culture broth containing 15% glycerol. The culture can then be aliquoted into 1 mL cryotubes, sealed, and placed at −80° C. for long-term viability retention. This procedure achieves acceptable viability upon recovery from frozen storage.

Organism production can be conducted using similar culture steps to banking, including medium composition and culture conditions. It can be conducted at larger scales of operation, especially for clinical development or commercial production. At larger scales, there can be several subcultivations of the bacterial composition prior to the final cultivation. At the end of cultivation, the culture is harvested to enable further formulation into a dosage form for administration. This can involve concentration, removal of undesirable medium components, and/or introduction into a chemical milieu that preserves the bacterial composition and renders it acceptable for administration via the chosen route. For example, a bacterial composition can be cultivated to a concentration of 10¹⁰ CFU/mL, then concentrated 20-fold by tangential flow microfiltration; the spent medium may be exchanged by diafiltering with a preservative medium consisting of 2% gelatin, 100 mM trehalose, and 10 mM sodium phosphate buffer. The suspension can then be freeze-dried to a powder and titrated.

After drying, the powder can be blended to an appropriate potency, and mixed with other cultures and/or a filler such as microcrystalline cellulose for consistency and ease of handling, and the bacterial composition formulated as provided herein.

In one embodiment, one or more of the populations of bacterial cells in the composition are co-cultured.

In some embodiments, the bacteria are not grown in a medium consisting of 0-5% yeast extract broth. In other embodiments, the bacteria are grown in 0-5% yeast extract broth with glucose or another metabolizable monosaccharide (e.g., fructose) or disaccharide (e.g., sucrose) in order to optimize production of the metabolites as described herein. In some embodiments, the concentration of glucose or metabolizable monosaccharide or disaccharide is 0.5-5%. In one embodiment, the medium comprises 3% yeast extract broth.

In some embodiments, corn steep liquor is added to the bacterial medium to optimize metabolite production (e.g., 0.5-5% corn steep liquor). Corn steep liquor is a byproduct of wet corn milling. Its components are soluble proteins, amino acids, carbohydrates, organic acids (e.g., lactic acid), vitamins, and minerals. It is sometimes combined with other ingredients in corn gluten feed and widely used in complete feeds for dairy and beef cattle, poultry, swine, and pet foods. Some corn steep liquor is used in the production of acetic acid, food acids, and fermentation processes. Some corn steep liquor is used in the pharmaceutical industry in the production of intravenous solutions and drugs, most notably antibiotics (penicillin). In certain embodiments, the concentration of corn steep liquor is 0.5-4%, 0.5-3%, 0.5-2%, 0.5-1%, 2-4%, 3%, 2-5%, 3-5%, 4-5%, 1-4%, or any range therebetween. In one embodiment the concentration of corn steep liquor is 3%.

Dosage, Administration and Formulations

In some embodiments, cells over a range of, for example, 2-5×10⁵, or more, e.g., 1×10⁶, 1×10⁷, 1×10⁸, 5×10⁸, 1×10⁹, 5×10⁹, 1×10¹⁰, 5×10¹⁰, 1×10¹¹ or more can be administered in a composition comprising a bacterium or collection of bacteria as described herein. The dosage range for the bacteria depends upon the potency, and includes amounts large enough to produce the desired effect, e.g., reduction in at least one symptom of a disease associated with mitochondrial dysfunction in a treated subject. The dosage should not be so large as to cause unacceptable adverse side effects. Generally, the dosage will vary with the type of illness, and with the age, condition, and sex of the patient. The dosage can be determined by one of skill in the art and can also be adjusted by the individual physician in the event of any complication.

For use in the various aspects described herein, an effective amount of cells in a composition as described herein comprises at least 1×10⁵ bacterial cells, at least 1×10⁶ bacterial cells, at least 1×10⁷ bacterial cells, at least 1×10⁸ bacterial cells, at least 1×10⁹ bacterial cells, at least 1×10¹⁰ bacterial cells, at least 1×10¹¹ bacterial cells, at least 1×10¹² bacterial cells or more. In some embodiments of the aspects described herein, the bacterial cells (e.g., isolated from rotting fruit) are expanded or maintained in culture prior to administration to a subject in need thereof. In one embodiment, the bacterial strain(s) is/are obtained from a microbe bank. In some embodiments, two or more bacterial strains are administered together, e.g., in a single admixture. However, it is specifically contemplated herein that two or more bacterial strains can be administered as separate dosage forms or sub-mixtures or sub-combinations of the strains. Thus, for a consortium of e.g., three members, the consortium can be administered, for example, as a single preparation including all three members (in one or more dosage units, e.g., one or more capsules) or as two or more separate preparations that, in sum, include all members of the given strains. While administration as a single admixture is preferred, a potential advantage of the use of e.g., individual units for each strain, is that the actual strains administered to any given subject can be tailored, if necessary, by selecting the appropriate combination of, for example, single species dosage units that together comprise the desired consortium.

In some embodiments, the compositions described herein can be administered in a form containing one or more pharmaceutically acceptable carriers. Suitable carriers are well known in the art and vary with the desired form and mode of administration of the composition. For example, pharmaceutically acceptable carriers can include diluents or excipients such as fillers, binders, wetting agents, disintegrators, surface-active agents, glidants, lubricants, and the like. Typically, the carrier may be a solid (including powder), liquid, or combinations thereof. Each carrier is preferably “acceptable” in the sense of being compatible with the other ingredients in the composition and not injurious to the subject. The carrier can be biologically acceptable and inert (e.g., it permits the composition to maintain viability of the biological material until delivered to the appropriate site).

Oral compositions can include an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, lozenges, pastilles, troches, or capsules, e.g., gelatin capsules. Oral compositions can also be prepared by combining a composition of the present disclosure with a food. In some embodiments, the bacterium/bacteria can be formulated in a food item. Some non-limiting examples of food items to be used with the methods and compositions described herein include: popsicles, cheeses, creams, chocolates, milk, meat, drinks, pickled vegetables, kefir, miso, sauerkraut, etc. In other embodiments, the food items can be juices, refreshing beverages, tea beverages, drink preparations, jelly beverages, and functional beverages; alcoholic beverages such as beers; carbohydrate-containing foods such as rice food products, noodles, breads, and pastas; paste products such as fish, hams, sausages, paste products of seafood; retort pouch products such as curries, food dressed with a thick starchy sauce, and Chinese soups; soups; dairy products such as milk, dairy beverages, ice creams, and yogurts; fermented products such as fermented soybean pastes, fermented beverages, and pickles; bean products; various confectionery products including biscuits, cookies, and the like, candies, chewing gums, gummies, cold desserts including jellies, cream caramels, and frozen desserts; instant foods such as instant soups and instant soy-bean soups; and the like. It is preferred that food preparations not require cooking after admixture with the bacterial strain(s) to avoid killing the microbes.

In one embodiment a food used for administration is chilled, for instance, iced flavored water. In certain embodiments, the food item is not a potentially allergenic food item (e.g., not soy, wheat, peanut, tree nuts, dairy, eggs, shellfish or fish). Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, primogel, or corn starch; a lubricant such as magnesium stearate or sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, orange flavoring, or other suitable flavorings. These are for purposes of example only and are not intended to be limiting.

Formulations suitable for oral administration may be provided as discrete units, such as tablets, capsules, cachets, syrups, elixirs, prepared food items, microemulsions, solutions, suspensions, lozenges, or gel-coated ampules, each containing a predetermined amount of the active compound; as powders or granules; as solutions or suspensions in aqueous or non-aqueous liquids; or as oil-in-water or water-in-oil emulsions.

The compositions described herein can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery. Formulations suitable for rectal administration include gels, creams, lotions, aqueous or oily suspensions, dispersible powders or granules, emulsions, dissolvable solid materials, douches, and the like. The formulations are preferably provided as unit-dose suppositories comprising the active ingredient in one or more solid carriers forming the suppository base, for example, cocoa butter. Suitable carriers for such formulations include petroleum jelly, lanolin, polyethyleneglycols, alcohols, and combinations thereof. Alternatively, colonic washes with the rapid recolonization deployment agent of the present disclosure can be formulated for colonic or rectal administration. The compositions can be prepared with carriers that will protect the bacteria against rapid elimination from the body, such as a controlled release formulation, including implants. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Such formulations can be prepared using standard techniques. The materials can also be obtained commercially from, for instance, Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art.

In some embodiments, a composition can be encapsulated or microencapsulated (e.g., enteric-coated formulations). For instance, when the composition is to be administered orally, the dosage form is formulated so the composition is not exposed to conditions prevalent in the gastrointestinal tract before the small intestine, e.g., high acidity and digestive enzymes present in the stomach. An enteric coating can be stable at low pH (such as in the stomach) and can dissolve at higher pH (for example, in the small intestine). Material that can be used in enteric coatings includes, for example, alginic acid, cellulose acetate phthalate, plastics, waxes, shellac, and fatty acids (e.g., stearic acid, palmitic acid). Enteric coatings are described, for example, in U.S. Pat. Nos. 5,225,202, 5,733,575, 6,139,875, 6,420,473, 6,455,052, and 6,569,457, all of which are herein incorporated by reference in their entirety. The enteric coating can be an aqueous enteric coating. Examples of polymers that can be used in enteric coatings include, for example, shellac (trade name EmCoat 120 N, Marcoat 125); cellulose acetate phthalate (trade names AQUACOAT™, AQUACOAT ECD™, SEPIFILM™, KLUCEL™, and ETOLOSE™); polyvinylacetate phthalate (trade name SURETERIC™); and methacrylic acid (trade name EUDRAGIT). The encapsulation of compositions for therapeutic use is known in the art. Encapsulation can include hard-shelled capsules, which can be used for dry, powdered ingredients, or soft-shelled capsules. Capsules can be made from aqueous solutions of gelling agents such as animal protein (e.g., gelatin), plant polysaccharides or derivatives like carrageenans and modified forms of starch and cellulose. Other ingredients can be added to a gelling agent solution such as plasticizers (e.g., glycerin and or sorbitol), coloring agents, preservatives, disintegrants, lubricants and surface treatment.

In one embodiment, an enteric coated probiotic composition as described herein is administered to a subject. In another embodiment, an enteric coated probiotic and prebiotic composition is administered to a subject.

Formulations of a bacterial composition or bacterial extract can be prepared by any suitable method, typically by uniformly and intimately admixing the bacterial cells with liquids or finely divided solid carriers or both, in the required proportions and then, if necessary, shaping the resulting mixture into the desired shape. In some embodiments, the bacterial strain(s) as described herein is/are combined with one or more additional probiotic organisms prior to treatment of a subject. As used herein, the term “probiotic” refers to microorganisms that form at least a part of the transient or endogenous flora and thereby exhibit a beneficial prophylactic and/or therapeutic effect on the host organism. Probiotics are non-pathogenic under normal circumstances and include, but are not limited to, those designated “Generally Regarded as Safe (GRAS)” by the U.S. Food & Drug Administration.

A nutrient supplement comprising the bacterium or bacterial consortium as described herein can include any of a variety of nutritional agents, including vitamins, minerals, essential and nonessential amino acids, carbohydrates, lipids, foodstuffs, dietary supplements, short chain fatty acids and the like. Preferred compositions comprise vitamins and/or minerals in any combination. Vitamins for use in a composition as described herein can include vitamins B, C, D, E, folic acid, K, niacin, and like vitamins. The composition can contain any or a variety of vitamins as may be deemed useful for a particular application, and therefore, the vitamin content is not to be construed as limiting. Typical vitamins are those, for example, recommended for daily consumption and in the recommended daily amount (RDA), although precise amounts can vary. The composition can preferably include a complex of the RDA vitamins, minerals and trace minerals as well as those nutrients that have no established RDA, but have a beneficial role in healthy human or mammal physiology. The preferred mineral format can include, for example, those that are in either the gluconate or citrate form which are more readily metabolized by lactic acid bacteria. Similar considerations can be employed to favor other classes of bacteria as needed. In a related embodiment, the compositions described herein are contemplated to comprise one or more bacteria or a bacterial consortium as described herein in combination with a viable lactic acid bacteria in combination with any material to be absorbed, including but not limited to nutrient supplements, foodstuffs, vitamins, minerals, medicines, therapeutic compositions, antibiotics, hormones, steroids, and the like compounds where it is desirable to insure efficient and healthy absorption of materials from the gastrointestinal tract into the blood. The amount of material included in the composition can vary widely depending upon the material and the intended purpose for its absorption, such that the composition is not to be considered as limiting.

The compositions as described herein can comprise from about 100 mg to about 100 g, alternatively from about 500 mg to about 50 g, and alternatively from about 1 g to about 40 g, of a prebiotic, per day or on a less than daily schedule.

Prior to administration of a bacterial composition, the patient may optionally have a pretreatment protocol with an antibiotic to prepare the gastrointestinal tract to receive the bacterial composition. In certain embodiments, the pretreatment protocol is advisable, such as when a patient has an acute infection with a highly resilient pathogen. In other embodiments, the pretreatment protocol is entirely optional, such as when a patient does not have an infection with a pathogen, or for example, when a pathogen causing an infection is not resilient, or the patient has had an acute infection that has been successfully treated but where the physician is concerned that the infection may recur. In these instances, the pretreatment protocol can enhance the ability of the bacterial composition to affect the patient's microbiome and/or enhance the therapeutic outcome. In an alternative embodiment, the subject is not pre-treated with an antibiotic.

As one way of preparing the patient for administration of the therapeutic microbes, at least one antibiotic can be administered to alter the bacteria in the patient. As another way of preparing the patient for administration, a standard colon-cleansing preparation can be administered to the patient to substantially empty the contents of the colon, such as used to prepare a patient for a colonoscopy. By “substantially emptying the contents of the colon,” is meant removing at least 75%, at least 80%, at least 90%, at least 95%, or about 100% of the ordinary volume of colon contents. Antibiotic treatment can precede a colon-cleansing protocol.

If a patient has received an antibiotic for treatment of an infection, or if a patient has received an antibiotic as part of a specific pretreatment protocol, in one embodiment the antibiotic should be stopped in sufficient time to allow the antibiotic to be substantially reduced in concentration in the gut before a bacterial composition is administered. In one embodiment, the antibiotic may be discontinued 1, 2, or 3 days before the administration of the bacterial composition. In one embodiment, the antibiotic can be discontinued 3, 4, 5, 6, or 7 antibiotic half-lives before administration of the bacterial composition. If the pretreatment protocol is part of treatment of an acute infection, the antibiotic may be chosen so that the infection is sensitive to the antibiotic, but the constituents in the administered bacterial composition are not sensitive to the antibiotic.

Any of the preparations described herein can be administered once on a single occasion or on multiple occasions, such as once a day for several days or more than once a day on the day of administration (including twice daily, three times daily, or up to five times daily). Or the preparation can be administered intermittently according to a set schedule, e.g., once weekly, once monthly, or when the patient relapses from the primary illness. In another embodiment, the preparation can be administered on a long-term basis to assure the maintenance of a protective or therapeutic effect. Note that while description above and elsewhere herein refer to formulations for delivery of bacteria, formulations comprising metabolites produced by such bacteria can be prepared and administered in a similar manner.

Excluded Bacteria:

As will be readily appreciated by one of skill in the art, a composition as described herein for treatment of disease will ideally not comprise one or more pathogenic bacteria. In one embodiment, a composition as described herein (e.g., a bacterial extract or a probiotic composition) does not include an organism conventionally classified as a pathogenic or opportunistic organism. It is possible that a function shared by all members of a given taxonomic group could be beneficial, e.g., for providing particular metabolites, yet for other reasons the overall effect of one or more particular members of the group is not beneficial and is, for example, pathogenic. Clearly, members of a given taxonomic group that cause pathogenesis, e.g., acute gastrointestinal pathologies, are to be excluded from the therapeutic or preventive methods and compositions described herein.

In one embodiment, the bacterial composition does not comprise at least one of Acidaminococcus intestinalis, Lactobacillus casei, Lactobacillus paracasei, Raoultella sp., and Streptococcus mitis. In another embodiment, the bacterial composition does not comprise any of these.

In another embodiment, the bacterial composition does not comprise at least one of Barnesiella intestinihominis, Lactobacillus reuteri, Enterococcus hirae, Enterococus faecium, or Enterococcus durans, Anaerostipes caccae, Clostridium indolis, Staphylococcus wameri, or Staphylococcus pasteuri, and Adlercreutzia equolifaciens. In another embodiment, the bacterial composition does not comprise any of these.

In another embodiment, the bacterial composition does not comprise at least one of Clostridium botulinum, Clostridium cadaveric, Clostridium chauvoei, Clostridium clostridioforme, Clostridium cochlearium, Clostridium difficile, Clostridium haemolyticum, Clostridium hastiforme, Clostridium histolyticum, Clostridium indolis, Clostridium irregulare, Clostridium limosum, Clostridium malenominatum, Clostridium novyi, Clostridium oroticum, Clostridium paraputrificum, Clostridium perfringens, Clostridium piliforme, Clostridium putrefaciens, Clostridium putrificum, Clostridium septicum, Clostridium sordellii, Clostridium sphenoides, and Clostridium tetani. In another embodiment, the bacterial composition does not comprise any of these.

In another embodiment, the bacterial composition does not comprise at least one of Escherichia coli and Lactobacillus johnsonii. In another embodiment, the bacterial composition does not comprise any of these.

In another embodiment, the bacterial composition does not comprise at least one of Clostridium innocuum, Clostridium butyricum, and Blautia producta (previously known as Peptostreptococcus productus). In another embodiment, the bacterial composition does not comprise any of these.

In another embodiment, the bacterial composition does not comprise at least one of Eubacteria, Fusobacteria, Propionibacteria, Escherichia coli, and Gemmiger.

In another embodiment, the compositions described herein do not comprise pathogenic bacteria in the Genera Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bacillus, multi-drug resistant bacteria, extended spectrum beta-lactam resistant Enterococci (ESBL), Carbapenem-resistant Enterobacteriaceae (CRE), or vancomycin-resistant Enterococci (VRE).

In other embodiments, the compositions described herein do not comprise pathogenic species or strains, such as Aeromonas hydrophila, Campylobacter fetus, Plesiomonas shigelloides, Bacillus cereus, Campylobacter jejuni, enteroaggregative Escherichia coli, enterohemorrhagic Escherichia coli, enteroinvasive Escherichia coli, enterotoxigenic Escherichia coli (such as, but not limited to, LT and/or ST), Escherichia coli 0157:H7, Helicobacter pylori, Klebsiellia pneumonia, Lysteria monocytogenes, Plesiomonas shigelloides, Salmonella spp., Salmonella typhi, Salmonella paratyphi, Shigella spp., Staphylococcus spp., Staphylococcus aureus, vancomycin-resistant enterococcus spp., Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, or Yersinia enterocolitica.

In one embodiment, the bacterial compositions or formulations as described herein do not comprise Klebsiella pneumoniae, Proteus mirabilis, Enterobacter cloacae, or Bilophila wadsworthia.

Efficacy Measurement

The term “effective amount” as used herein refers to the amount of a population of bacterial cells or their components or metabolites needed to alleviate at least one or more symptoms of a disease associated with mitochondrial dysfunction and relates to a sufficient amount of a composition to provide the desired effect. An effective amount as used herein also includes an amount sufficient to prevent or delay the development of a symptom of the disease, alter the course of a symptom of the disease (for example but not limited to, slow the progression of a symptom of the disease, such as myopathy), or reverse a symptom of the disease. It is understood that for any given case, an appropriate “effective amount” can be determined by one of ordinary skill in the art using routine experimentation. Given the intricacies of the body and the nature of cell establishment, the “effective amount” of cells may vary among different patients, however one can easily determine in hindsight if the amount of cells administered was indeed an ‘effective amount.” Thus, further treatments can be modified accordingly. Note that long-term colonization or establishment, while often desirable, is not necessary for effective treatment as regular administration can achieve effective treatment as well.

The efficacy of treatment can be determined by the skilled clinician. However, a treatment is considered “effective treatment,” as the term is used herein, if any one or all of the symptoms, or other clinically accepted symptoms or markers of a disease associated with mitochondrial dysfunction are reduced, e.g., by at least 10% following treatment with a composition comprising bacterial cells or a bacterial extract as described herein. Methods of measuring these indicators are known to those of skill in the art and/or described herein.

In one embodiment, effective treatment is determined by a reduction in the dose of a conventional pharmacological treatment required to maintain adequate control of symptoms of a disease associated with mitochondrial dysfunction.

In some embodiments, the subject is further evaluated using one or more additional diagnostic procedures, for example, by medical imaging, physical exam, laboratory test(s), clinical history, family history, genetic test, and the like. Medical imaging is well known in the art. As such, the medical imaging can be selected from any known method of imaging, including, but not limited to, ultrasound, computed tomography scan, positron emission tomography, photon emission computerized tomography, and magnetic resonance imaging.

The present invention may be as described in any one of the following numbered paragraphs:

1. A composition comprising a measured amount of one or more bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

2. The composition of paragraph 1, wherein the bacterium is from the Acetobacteriaceae family.

3. The composition of paragraph 1 or 2, wherein the bacterium is Gluconobacter spp (e.g., Gluconobacter EBT 405), Acetobacter spp., Gluconoacaetobacter spp., Acidomonas spp, Ameyamaea spp., Asaia spp., Granulibacter spp., Kozakia spp., Neoasaia spp., Neokomagataea spp., Saccharibacter spp., Swaminathania spp., or Tanticharoenia spp.

4. The composition of any one of paragraphs 1-3, wherein one or more of the nucleic acid sequences are exogenous nucleic acid sequences.

5. The composition of any one of paragraphs 1-4, wherein the bacterium comprises and expresses nucleic acid sequences encoding each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

6. The composition of any one of paragraphs 1-5, wherein the measured amount of the one or more bacterium is lyophilized.

7. The composition of any one of paragraphs 1-6, wherein the measured amount is an amount effective to induce expression and/or activity of mitochondrial transcription factor A (TFAM), or peroxisome proliferator activated receptor gamma coactivator 1 (PGC) in a human cell upon administration to a subject in need thereof.

8. The composition of paragraph 7, wherein the amount effective to induce expression and/or activity of TFAM, or PGC in a human cell is 1×10⁶ bacteria.

9. The composition of any one of paragraphs 1-8, wherein the composition further comprises one or more added bacterial metabolites selected from the group consisting of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

10. The composition of any one of paragraphs 1-9, wherein the bacterium is viable, attenuated or heat-inactivated.

11. The composition of any one of paragraphs 1-10, wherein the composition is formulated as a food, a beverage, a feed composition, a probiotic, a nutritional supplement, or a pharmaceutical composition.

12. The composition of any one of paragraphs 1-11, which further comprises a prebiotic.

13. The composition of paragraph 12, wherein the prebiotic comprises a fructooligosaccharide, an inulin, an isomaltooligosaccharide, lactilol, lactosucrose, lactulose, a soy oligosaccharide, a transgalactooligosaccharide or a xylooligosaccharide.

14. The composition of any one of paragraphs 1-13, further comprising a pharmaceutically acceptable carrier.

15. The composition of any one of paragraphs 1-14, wherein the composition is formulated for oral administration.

16. The composition of paragraph 15, wherein the composition is an enteric-coated formulation.

17. A composition comprising a therapeutically effective amount of an extract or fraction derived from at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding an enzyme selected from the group consisting of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

18. The composition of paragraph 17, wherein the at least one bacterium comprises and expresses each of the enzymes membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

19. The composition of paragraph 17 or 18, wherein the extract or fraction comprises one or more metabolites selected from gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

20. The composition of any one of paragraphs 17-19, wherein the extract or fraction is from bacterial cells cultured in a medium comprising: (i) standard Lysogeny broth (1% tryptone, 0.5% yeast extract, and 1% sodium chloride) containing 1% glucose, (ii) standard Hestrin-Schramm broth (D-glucose 2%, 0.5% yeast extract, 0.5% peptone, 0.27% disodium phosphate, 0.115% citric acid) or (iii) CaCO₃ medium comprising 8% glucose, 0.5% yeast extract, 0.2% mannitol, 0.05% magnesium sulphate, and 10% calcium carbonate.

21. The composition of any one of paragraphs 17-20, wherein the extract or fraction comprises metabolites or bacterial byproducts that promote ATP production in at least one cell type of a host mammal administered the composition.

22. The composition of any one of paragraphs 17-21, wherein the extract or fraction does not comprise viable bacterial cells.

23. The composition of any one of paragraphs 17-22, wherein the extract or fraction lacks detectable bacteria.

24. The composition of any one of paragraphs 17-23, wherein the extract or fraction further comprises attenuated or heat-inactivated bacteria.

25. The composition of any one of paragraphs 17-24, wherein the bacterium is from the Acetobacteriaceae family.

26. The composition of paragraph 25, wherein the bacterium is Gluconobacter spp (e.g., Gluconobacter EBT 405), Acetobacter spp., Gluconoacaetobacter spp., Acidomonas spp, Ameyamaea spp., Asaia spp., Granulibacter spp., Kozakia spp., Neoasaia spp., Neokomagataea spp., Saccharibacter spp., Swaminathania spp., or Tanticharoenia spp.

27. The composition of any one of paragraphs 17-26, wherein one or more of the nucleic acid sequences is/are an exogenous nucleic acid sequence(s).

28. The composition of any one of paragraphs 17-27, wherein the composition is formulated as a food, a beverage, a feed composition, a nutritional supplement, or a pharmaceutical composition.

29. The composition of any one of paragraphs 17-28, wherein the composition further comprises a pharmaceutically acceptable carrier.

30. The composition of any one of paragraphs 17-29, wherein the composition is formulated for oral administration.

31. A method for increasing cellular ATP production in at least one cell type of a subject in need thereof, the method comprising administering to the subject a composition comprising an amount of at least one non-pathogenic bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, effective to increase cellular ATP production in at least one cell type.

32. The method of paragraph 31, wherein the at least one bacterium expresses each of membrane-bound of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

33. The method of any one of paragraphs 31-32, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

34. The method of any one of paragraphs 31-33, wherein the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

35. The method of any one of paragraphs 31-34, wherein one or more of the nucleic acid sequences is exogenous to the bacterium.

36. The method of any one of paragraphs 31-35, wherein the activity of complex I and/or complex II of the mitochondrial electron transport chain is increased in the one or more cell types.

37. The method of any one of paragraphs 31-36, wherein the administering increases mitochondrial membrane potential.

38. The method of any one of paragraphs 31-37, wherein the subject is human.

39. The method of any one of paragraphs 31-38, wherein expression of peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1a), and/or mitochondrial transcription factor A (TFAM) is increased.

40. The method of any one of paragraphs 31-39, wherein AMP-activated protein kinase (AMPK) phosphorylation levels, nuclear respiratory factor-2 (Nrf2) protein levels, PGCα mRNA levels TFAM mRNA levels and/or mitochondrial DNA replication is increased.

41. The method of any one of paragraphs 31-40, wherein the mitochondrial DNA copy numbers (mtDNA) is increased.

42. The method of any one of paragraphs 31-41, wherein the method increases the developmental growth rate of a subject carrying a mutations in mitochondrial respiratory Complex I NADH:ubiquinone reductase.

43. The method of any one of paragraphs 31-42, wherein the expression of at least one mitochondrial β-oxidation enzyme is increased.

44. The method of paragraph 43, wherein the at least one mitochondrial β-oxidation enzyme is B0303.3, cpt-2, cpt-1, ech-1.2, or acdh-7.

45. The method of any one of paragraphs 31-44, wherein the longevity of the subject is increased.

46. The method of any one of paragraphs 31-45, wherein mitochondrial biogenesis is maintained or increased.

47. The method of any one of paragraphs 31-46, wherein cellular ATP production is increased by at least 10% compared to the cellular ATP production prior to administration of the composition.

48. A method for making a bacterial extract, the method comprising culturing at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II in a medium comprising: (i) standard Lysogeny broth (1% tryptone, 0.5% yeast extract, and 1% sodium chloride) containing 1% glucose, (ii) standard Hestrin-Schramm broth (D-glucose 2%, 0.5% yeast extract, 0.5% peptone, 0.27% disodium phosphate, 0.115% citric acid) or (iii) CaCO₃ medium comprising 8% glucose, 0.5% yeast extract, 0.2% mannitol, 0.05% magnesium sulphate, and 10% calcium carbonate.

49. The method of paragraph 48, wherein the at least one bacterium comprises and expresses nucleic acid sequences encoding each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

50. The method of paragraph 48 or 49, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.

51. A composition comprising an amount of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid effective to increase cellular ATP production in at least one cell type of a host mammal administered the composition.

52. A composition comprising an amount of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid effective to increase the expression and/or activity of mitochondrial transcription factor A (TFAM), or peroxisome proliferator activated receptor gamma coactivator 1 (PGC) in at least one cell type of a human subject administered the composition.

53. The composition of paragraph 51 or 52, wherein the composition comprises a bacterial extract or active fraction thereof.

54. The composition of paragraph 51, 52 or 53, wherein the composition is formulated as a food, a beverage, a feed composition, a nutritional supplement, or a pharmaceutical composition.

55. A method of treating Parkinson's disease, the method comprising administering to a subject having Parkinson's disease, a composition comprising a therapeutically effective amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, thereby reducing at least one symptom of Parkinson's disease.

56. The method of paragraph 55, wherein the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

58. The method of paragraph 55 or 56, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid

59. The method of any one of paragraphs 55-58, wherein (i) the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid and/or (ii) the bacterium comprises Gluconobacter EBT 405.

60. The method of any one of paragraphs 55-59, wherein the at least one symptom is selected from the group consisting of: tremor, sleep disturbance, mobility impairment, involuntary movement, muscle rigidity, rhythmic muscle contraction, slow bodily movement, slow shuffling gait, fatigue, dizziness, impaired balance, restlessness, amnesia, confusion, dementia, cognitive impairment, impaired speech, anxiety, apathy, distorted or loss of sense of smell, urinary incontinence, reduced facial expression, weight loss and constipation.

61. A method of treating a mitochondrial electron transport chain disorder, the method comprising administering to a subject having a mitochondrial electron transport chain disorder, a composition comprising a therapeutically effective amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, thereby reducing at least one symptom of the mitochondrial electron transport chain disorder.

62. The method of paragraph 61, wherein the mitochondrial electron transport chain disorder comprises a disorder or impaired activity in Complex I and/or Complex II.

63. The method of paragraph 61 or 62, wherein the mitochondrial electron transport chain disorder is NADH dehydrogenase (NADH-CoQ reductase) deficiency, succinate dehydrogenase deficiency, Leigh Disease, mitochondrial DNA depletion, or mitochondrial insufficiency.

64. The method of any one of paragraphs 61-63, wherein the at least one symptom is selected from the group consisting of: myopathy, mitochondrial encephalomyopathy, failure to thrive, developmental delay, hypotonia, lethargy, respiratory failure, ataxia, myoclonus, lactic acidosis, seizures, fatigue, nystagmus, poor reflexes, difficulty eating or swallowing, breathing difficulties, ataxia, congenital myopathy, infantile myopathy and hepatopathy.

65. The method of any one of paragraphs 61-64, wherein the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

66. The method of any one of paragraphs 61-65, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

67. The method of any one of paragraphs 61-66, wherein the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

68. A method of treating a peroxisomal disorder, the method comprising administering to a subject having a peroxisomal disorder, a composition comprising a therapeutically effective amount of at least one bacterium that comprises one or more nucleic acid sequences such that the bacterium expresses the following enzymes: membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or a bacterial extract thereof, thereby reducing at least one symptom of the peroxisomal disorder.

69. The method of paragraph 68, wherein the peroxisomal disorder is Zellweger syndrome spectrum (PBD-ZSD), or rhizomelic chondrodysplasia punctate type 1 (RCDP1).

70. The method of paragraph 68 or 69, wherein the PBD-ZSD is infantile Refsum disease, neonatal adrenoleukodystrophy, or Zellweger syndrome.

71. The method of any one of paragraphs 68-70, wherein the at least one symptom is selected from the group consisting of: skeletal and craniofacial dysmorphism, liver dysfunction, progressive sensorineural hearing loss and retinopathy.

72. The method of any one of paragraphs 68-71, wherein the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

73. The method of any one of paragraphs 68-72, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

74. The method of any one of paragraphs 68-73, wherein the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

75. A method for increasing the biogenesis of cellular mitochondria or peroxisomes, the method comprising administering to a subject, a composition comprising an amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or a fraction or extract thereof, effective to increase the biogenesis of cellular mitochondria or peroxisomes.

76. The method of paragraph 75, wherein the size and/or number of peroxisomes is increased.

77. The method of paragraph 75 or 76, wherein mitochondrial activity is increased.

78. The method of paragraph 75, 76, or 77, wherein the at least one bacterium expresses each of encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

79. The method of any one of paragraphs 75-78, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

80. The method of any one of paragraphs 75-79, wherein the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

81. A method of treating Alzheimer's disease, the method comprising administering to a subject having Alzheimer's disease, a composition comprising a therapeutically effective amount of at least one bacterium that comprises and expresses one or more nucleic acid sequences encoding one or more of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, thereby reducing at least one symptom of Alzheimer's disease.

82. The method of paragraph 81, wherein the at least one bacterium expresses each of membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II.

83. The method of paragraph 81 or 82, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid

84. The method of paragraph 81, 82 or 83, wherein the at least one bacterium produces each of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid.

85. The method of any one of paragraphs 81-84, wherein the at least one symptom is selected from the group consisting of: cognitive decline, confusion, delusion, disorientation, forgetfulness, difficulty concentrating, inability to generate new memories, inability to do simple math, inability to recognize common items, aggression, agitation, irritability, meaningless repetition of own words, personality changes, restlessness, lack of restraint, wandering, anger, apathy, general discontent, loneliness, mood swings, depression, hallucination, paranoia, loss of appetite, inability to combine muscle movements and jumbled speech.

86. The method of any one of paragraphs 81-85, wherein the bacterium comprises Gluconobacter EBT 405.

EXAMPLES

The following provides non-limiting Examples demonstrating and supporting the technology as described herein.

Example 1: Results

Six microbes that suppress the slow developmental growth rate phenotype of three mitochondrial mutants of C. elegans: spg-7(ad2249)¹, gas-1(fc21)², and nduf-7(et19)³ were identified using a qualitative visual screen. spg-7 encodes a homolog of AFG3L2, which is a conserved m-AAA metalloprotease¹. Along with another m-AAA metalloprotease paraplegin, AFG3L2 is involved in the removal of abnormal proteins from the mitochondria and thus maintenance of the mitochondrial proteome. nduf-7 encodes NADH-ubiquinone oxidoreductase Fe—S, which is a component of complex I in the mitochondrial electron transport chain³. gas-1 encodes a NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, which is a component of complex I in the mitochondrial electron transport chain². gas-1 (fc21) mutant animals exhibit significantly decreased mitochondrial mass and membrane potential and thus, reduced respiratory capacity^(4,5 6) spg-7(ad2249), gas-1(fc21), and nduf-7(et19) mutants grow at a significantly slower rate compared to the wildtype animals (FIG. 1A) when fed on E. coli OP50. E. coli OP50 is the standard microbial strain on which Caenorhabditis elegans are typically grown in the laboratory. A screen was performed to test whether any of the microbes that are naturally associated with C. elegans in the wild can modify the slow growth phenotype of the mitochondrial mutants. In the screen, ˜200 strains of wild microbes were fed individually to synchronized L1-stage spg-7(ad2249), gas-1 (fc21), and nduf-7(et19) mutants. Mutant animals that grew at a significantly faster rate compared to the animals fed on E. coli OP50 (FIG. 5A) were identified. In this screen, 6 microbes were identified that partially suppress the slow growth phenotype of the mitochondrial mutants. This study focuses on three of the microbes: Gluconacetobacter spp, Acetobacter spp, and Gluconobacter spp (FIG. 5A). Each of these microbes belong to the family Acetobacteraceae of the phylum Proteobacteria and are characterized by the ability to oxidize sugars or ethanol and produce acetic acid during fermentation⁷. They are naturally present in sugary and acidic niches such as fruits' and particularly in fermented beverages such as natural Apple cider vinegar⁹ and Kombucha¹⁰. Interestingly, it was found that these three bacteria (i.e., Gluconobacter, Acetobacter, and Gluconoacetobacter) were able to accelerate the developmental growth rate of even wildtype animals (FIGS. 5B-5D). Among the three species, Gluconacetobacter spp were comparatively better in accelerating the developmental growth rate (FIGS. 5A-5B). To determine specifically how Gluconacetobacter spp enhance developmental growth rate, the developmental acceleration rate was examined at each larval stage. It was found that Gluconacetobacter spp feeding specifically shortened the time taken for animals to reach egg-laying adult stage from L4-larval stage (FIGS. 5E-5F).

To test whether the enhancement of developmental growth rate was general for all mitochondrial mutants, mutations in other mitochondrial respiratory chain namely mev-1(kn1) and isp-1(qm150) were tested. mev-1 encodes a subunit of succinate-coenzyme Q oxidoreductase in the complex II of mitochondrial electron transport chain¹¹. isp-1 is an iron sulfur protein (isp-1) of cytochrome bc1 complex (complex 111)¹² . Gluconacetobacter spp feeding failed to suppress the slow developmental growth rate of mev-1(kn1) and isp-1(qm150) mutants, indicating that enhancement of complex I and/or complex II activity is a likely mode-of-action. It was hypothesized that Gluconacetobacter spp feeding might enhance the developmental growth rate of wildtype and the mitochondrial mutants by increasing the mitochondrial ATP production. To test this hypothesis, a transgenic firefly luciferase-expressing C. elegans strain¹³ was used for rapid in vivo assessment of the ATP levels. Transgenic luciferase expressing strain fed on Gluconacetobacter spp had higher bioluminescence compared to the animals fed on E. coli OP50, indicating increased ATP content (FIG. 1B). This result was confirmed using an in vitro ATP determination assay (FIG. 1C). An increase in bioluminescence was observed as quickly as within 6 hours of initiating feeding with Gluconacetobacter spp (FIG. 5G). Further, it was found that the ATP levels were reduced in spg-7(ad2249) mutant fed on E. coli OP50 compared to the wildtype animals fed on E. coli OP50. In addition, Gluconacetobacter spp feeding was able to restore the ATP content of spg-7(ad2249) mutant (FIG. 1D). Similarly, it was found that Gluconacetobacter spp feeding was able to partially restore the ATP content of nduf-7(et19) mutant (FIG. 1E).

It was found that the mitochondrial membrane potential was significantly decreased in spg-7(ad2249), gas-1(fc21), and nduf-7(et19) mutants fed on E. coli OP50 compared to the wildtype animals fed on E. coli OP50 as assessed using Mitotracker™ CMXRos (FIG. 1F). Mitotracker™ CMXRos stains mitochondria and its accumulation in live cells is dependent upon membrane potential. Gluconacetobacter spp feeding was able to partially restore the mitochondrial membrane potential of spg-7(ad2249), gas-1(fc21), and nduf-7(et19) mutants (FIG. 1F). Using another dye, Tetramethylrhodamine, ethyl ester (TMRE), which is sequestered by active mitochondria, it was found that spg-7(ad2249) mutants fed on Gluconacetobacter spp had significantly increased dye levels compared to animals fed on E. coli OP50 (FIG. 5H) indicating that the mitochondrial membrane potential was increased.

Next, the effect of different mitochondrial poisons on the increased ATP production phenotype of animals fed on Gluconacetobacter spp was assessed. It was found that animals fed on Gluconacetobacter spp and treated with Rotenone or Paraquat or Sodium Azide had significantly higher levels of bioluminescence compared to animals fed on E. coli OP50 and treated with Rotenone or Paraquat or Sodium Azide (FIGS. 1G-1H; FIG. 5I). Both Paraquat (1,1′-dimethyl-4,4′-bipyridinium dichloride) and Rotenone are inhibitors of complex I in the mitochondrial electron transport chain while Sodium Azide and Antimycin are inhibitors of complex III.

It was found that animals fed on Gluconacetobacter spp were more resistant to Rotenone or Paraquat than animals fed on E. coli OP50 (FIG. 6A). However, animals fed on Gluconacetobacter spp were not more resistant to Sodium Azide or Antimycin compared to animals fed on E. coli OP50 (FIG. 6A).

The unfolded protein response of the mitochondria (UPR^(mt)) is initiated by mitochondrial stress and activates the expression of several nuclear genes, including the hsp-6 mitochondrial chaperone¹⁴. Using a hsp-6::gfp transgenic animal strain, it was determined whether Gluconacetobacter spp affects UPR^(mt) induction. Transgenic hsp-6::gfp animals fed on E. coli OP50 or Gluconacetobacter spp were treated with either MPP+ or 6-OHDA or Paraquat and induction of GFP expression was assessed after 24 hours of treatment. MPTP [1-methyl-4-phenylpyridinium (MPP+)] and 6-hydroxydopamine (6-OHDA) are neurotoxins that induce ROS production and are used in animal models of Parkinson's Disease (PD). While worms fed E. coli OP50 and treated with either MPP+ or 6-OHDA or Paraquat induced GFP expression, worms fed on Gluconacetobacter spp failed to induce GFP expression (FIG. 2A). Genetic mutations in gas-1(fc21), nduf-7(et19), mev-1(kn1) and isp-1(qm150) induced hsp-6::gfp expression constitutively. Feeding these mutants on Gluconacetobacter spp did not suppress the hsp-6::gfp expression. While the induction of hsp-6::gfp during UPR^(mt) is mediated by the ATFS-1 transcription factor¹⁵, a subset of the genes upregulated in UPR^(mt) are activated in an ATFS-1 independent fashion. Recently, tbb-6, which encodes an uncharacterized β-tubulin, was shown to be upregulated independently of ATFS-1 following mitochondrial ETC disruption¹⁶. A tbb-6::gfp transgenic strain was generated and it was found this GFP was induced in the spg-7(ad2249) mutant (FIG. 6B; FIG. 2B). Feeding spg-7(ad2249); tbb-6::gfp animals on Gluconacetobacter spp suppressed the tbb-6::gfp expression (FIG. 6B; FIG. 2B).

To address how Gluconacetobacter spp feeding improves mitochondrial function, a variety of transgenic worm strains were tested, including worms that carry a construct encoding a fusion protein comprising a GFP reporter protein and a gene product that is involved in stress response, mitochondrial activity, peroxisomal function, innate immune response, and different signaling pathways (Table 1; FIGS. 2C-2K; FIGS. 6C-6L; FIGS. 7A-7D).

TABLE 1 Transcriptional GFP fusion gene Gene description cyp-35B1 Cytochrome P450 haf-7 ABC-type multidrug transport system ugt-61 UDP-glucuronosyl and UDP-glucosyl transferase pgp-3 ABC-type multidrug transport system mrp-2 ABC-type multidrug transport system abch-1 ABC-type multidrug transport system pmp-4 ABC-type multidrug transport system ugt-58 UDP-glucuronosyl and UDP-glucosyl transferase dhs-9 short-chain dehydrogenases/reductases family (SDR) cyp-37A1 Cytochrome P450 dhs-19 short-chain dehydrogenases/reductases family (SDR) cyp-34A9 Cytochrome P450 cyp-14A3 Cytochrome P450 ugt-8 UDP-glucuronosyl and UDP-glucosyl transferase cyp-13a7 Cytochrome P450 pgp-4 ABC-type multidrug transport system cyp-31a3 Cytochrome P450 pgp-6 ABC-type multidrug transport system cyp-25a2 Cytochrome P450 ugt-22 UDP-glucuronosyl and UDP-glucosyl transferase pgp-9 ABC-type multidrug transport system pgp-5 ABC-type multidrug transport system sod-3 Superoxide dismutase/daf-16 target gst-4 Glutathione S-transferase/oxidative stress reporter gcs-1 Gamma GlutamylCysteine Synthetase/oxidative stress reporter hsp-60 Mitochondrial specific chaperone of GroE/Hsp10/60 family hsp-4 Heat shock response 70 (hsp70) protein/ Endoplasmic reticulum stress reporter hsp-6 Mitochondrion-specific chaperone of the DnaK/Hsp70family/mitochondrial stress reporter nlp-29 Neuropeptide like protein/Anti-fungal innate immune response reporter clec-60 C-type lectin family/innate immune response reporter irg-1 Innate immune response reporter hsp-16.2 Heat shock protein of hsp16/hsp20/alphaB- crystallin (HSP16) family/heat shock reporter nhr-57 Nuclear hormone receptor; hypoxia stress reporter rpt-3 triple A ATPase subunit of the 26S proteasome's 19S regulatory particle (RP) base subcomplex fat-7 delta-9 fatty acid desaturase tbb-6 human TUBB8 (tubulin beta 8 class VIII) hphd-1 human ADHFE1 (alcohol dehydrogenase, iron containing 1) B0303.3 3-Keto-coA thiolase beta-subunit of Trifunctional protein (HADHB) prx-11 vertebrate peroxisomal membrane protein 11C cpt-2 carnitine palmitoyltransferase acox-1.2 ACOX1 (acyl-CoA oxidase 1) ech-1.2 enoyl-CoA hydratases/long-chain 3-hydroxyacyl- CoA dehydrogenases acdh-7 ACADM (acyl-CoA dehydrogenase, C-4 to C-12 straight chain) prx-6 Pex6 (peroxisomal biogenesis factor 6) cpt-1 Carnitine Palmitoyltransferase I icl-1 isocitrate lyase/malate synthase, an enzyme known to function in the glyoxylate cycle lgg-1 ortholog of Saccharomyces cerevisiae Atg8p and mammalian MAP-LC3 UbV-gfp a UFD model substrate in which a noncleavable ubiquitin is N-terminally fused to GFP (UbV- GFP) lipl-1 human Lipases family including LIPF hsp-70 heat-shock protein that is a member of the hsp70 family of molecular chaperones ftn-2 ferritin heavy chain homolog ftn-1 ferritin heavy chain homolog fzo-1 GTPase orthologous to MFN1(Mitofusin)/FZO1 crtc-1 CREB-regulated transcriptional coactivator orthologous to mammalian CRTCs cts-1 citrate synthase acdh-1 Short-chain acyl-CoA dehydrogenase acdh-2 short-chain acyl-CoA dehydrogenase acdh-11 acyl-CoA dehydrogenase ads-1 AGPS (alkylglycerone phosphate synthase agxt-1 Alanine-Glyoxylate aminotransferase (AGXT) acox-1.6 ACOX1 (acyl-CoA oxidase 1) nhr-64 NR2 subfamily of nuclear receptors that contains Drosophila and human HNF4 daf-22 ortholog of human sterol carrier protein SCP2 nhr-69 NR2 subfamily of nuclear receptors that contains Drosophila and human HNF4 spg-20 human SPG20 (spastic paraplegia 20 (Troyer syndrome) cyp-29A2 CYP19A1 (cytochrome P450 family 19 subfamily A member 1) dhs-28 human 17-BETA-HYDROXYSTEROID DEHYDROGENASE 4 (HSD17B4 mtl-1 metallothioneins, small, cysteine-rich, metal- binding proteins kap-1 kinesin-associated protein C01H6.4 N,N-dimethylaniline monooxygenase activity tmem-135 TMEM135 (transmembrane protein 135) C53B4.3 Solute Carrier Family 22 (Organic Cation Transporter), Member 18 far-3 Fatty Acid/Retinol binding protein irg-4 CUB-like domain-containing protein irg-5 Infection Response Gene lys-7 antimicrobial lysozyme encoded by the LYS4 abf-1 antibacterial factor ASABF abf-3 antibacterial factor ASABF spp-7 SPP-protein family, called caenopores lys-1 putative lysozyme dod-22 human EPHX1 (epoxide hydrolase 1) F55G11.7 human EPHX1 (epoxide hydrolase 1) K08D8.5 CUB-like domain-containing protein clec-85 C-type LECtin F10A3.4 Nematode-specific gene

In this screen, it was found that Gluconacetobacter spp feeding induced the expression of a subset of genes required for either mitochondrial function or peroxisomal activity. These include B0303.3 (ortholog of human HADHB [3-Ketoacyl-coA Thiolase beta subunit]) (FIG. 2D; FIG. 6H), prx-11 (ortholog of human PEX11G [peroxisomal biogenesis factor 11G]) (FIG. 2E), cpt-2 (ortholog of human CPT2 [Carnitine Palmitoyl transferase]) (FIG. 2F; FIG. 6C), acox-1.2 (ortholog of human ACOX1 [Acyl CoA oxidase 1]) (FIG. 2G; FIG. 6D; FIG. 6J), ech-1.2 (ortholog of human HADHA [3-Ketoacyl-coA Thiolase alpha subunit]) (FIG. 2H; FIG. 6G), acdh-7 (ortholog of human ACADM [Acyl-CoA dehydrogenase, medium-chain]) (FIG. 2I; FIG. 6F, FIG. 6I), pmp-4 (ortholog of human ABCD1 [peroxisomal membrane ABC transporter]) (FIG. 2J; FIG. 6E), prx-6 (ortholog of human PEX6 [peroxisomal biogenesis factor 6]) (FIG. 2K), cpt-1 (ortholog of human CPT1 [Carnitine Palmitoyl transferase]) (FIG. 6K), and icl-1 (encodes isocitrate lyase/malate synthase) (FIG. 7A). Expression of one gene, hphd-1 (an ortholog of Human ADHFE1 [Alcohol dehydrogenase]) was significantly reduced in worms fed on Gluconacetobacter spp (FIG. 2C). CPT (carnitine 0-palmitoyltransferase) and ACADM (medium chain acyl CoA dehydrogenase) each play a pivotal role in mitochondrial fatty acid uptake and β-oxidation, two critical steps for energy production from fatty acids. Similarly, HADHA and HADHB encode the alpha and beta subunit of the mitochondrial hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), which catalyzes mitochondrial beta-oxidation of long chain fatty acids. ACOX1 catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs and is the first enzyme of the peroxisomal fatty acid beta-oxidation pathway. ICL-1 functions in the glyoxylate shunt, which converts isocitrate and acetyl-CoA to succinate, malate, and CoA using glyoxylate as an intermediate″. It was found that the Gluconacetobacter spp feeding induced cpt-2::gfp and that ech-1.2::gfp expression was dependent on tcer-1 (ortholog of TCERG1 [Transcription elongation regulator 1])^(18,19) (FIGS. 2F & 2H) while acox-1.2 (FIG. 2G), acdh-7 (FIG. 2I), pmp-4 (FIG. 2J), and prx-6 (FIG. 2K), expression was dependent on nhr-49 (encodes a nuclear hormone receptor with sequence similarity to HNF4a but functionally resemble more like peroxisome proliferator-activated receptor alpha (PPARα)²⁰. tcer-1(tm1452) and nhr-49(nr2041) animals fed on Gluconacetobacter spp feeding grew slower compared to wildtype worms fed on Gluconacetobacter spp (FIG. 3A) indicating that TCER-1 and NHR-49 activities promote accelerated developmental growth rate. Intestine-specific overexpression of nhr-49 was sufficient to accelerate growth rate of nhr-49(nr2041) mutants fed on Gluconacetobacter spp (FIG. 7E). Further, a strong induction of nhr-49::gfp was observed in the worms fed on Gluconacetobacter spp (FIG. 7F). To test whether NHR-49 itself is sufficient to accelerate developmental growth rate, gain-of-function alleles were determined in nhr-49(et7), nhr-49(et8), nhr-49(et13)²¹. None of these strains had accelerated growth rate phenotype when fed on E. coli OP50, while they still showed accelerated growth when fed on Gluconacetobacter spp.

In addition, a strong nuclear localization of TCER-1::GFP was observed in the intestinal cells of worms fed on Gluconacetobacter spp compared to worms fed on E. coli OP50 (FIG. 7G).

Since genes associated with peroxisomal function were upregulated in response to Gluconacetobacter spp feeding, it was tested whether RNAi of peroxisomal genes affect the accelerated developmental growth rate phenotype. RNAi of prx-5 (ortholog of PXR1 or PEX5 [human receptor for type I peroxisomal targeting signal protein]) or prx-11 (ortholog of human PEX11G [peroxisomal biogenesis factor 11G]) suppressed the accelerated developmental growth rate phenotype of wildtype worms fed on Gluconacetobacter spp (FIG. 3A). It was found that RNAi of tcer-1, nhr-49, and prx-5 suppressed the Gluconacetobacter spp feeding-induced increase in bioluminescence phenotype (FIG. 3B), indicating that these genes are required for increased ATP production upon Gluconacetobacter spp feeding. Further, RNAi of nhr-49 or prx-5 was able to suppress the accelerated developmental progression phenotype of spg-7(ad2249) and nduf-7(et19) mutant worms fed on Gluconacetobacter spp (FIGS. 3C-3D). Compared to wildtype worms, spg-7(ad2249) mutant have reduced mitochondrial membrane potential as assessed using Mito CMXRos and this reduction was further exacerbated by nhr-49 RNAi (FIG. 3E). A partial reduction of mitochondrial membrane potential was observed in wildtype worms fed on nhr-49 RNAi (FIG. 3E).

To examine the effect of Gluconacetobacter spp feeding on the mitochondrial morphology, a transgenic strain was used that expresses a fusion protein of C. elegans mitochondrial import receptor subunit TOMM-20 and monomeric red fluorescent protein (mRFP) and the expression is driven in body wall muscle cells by the myo-3 promoter²². In the transgenic worms fed on Gluconacetobacter spp, the mitochondria appear to be more fused compared to the worms fed on E. coli OP50 (FIG. 3F). Using Rhodamine 6G dye, which stains mitochondria, it was determined that the mitochondria in the hypodermis of worms fed on Gluconacetobacter spp appear more fused compared to worms fed on E. coli OP50 (FIG. 7H). Mitochondria are dynamic organelles that constantly undergo fusion and fission events. The elongated morphology is associated with increased ATP production efficiency²³ and decreased ROS formation²⁴. Thus, without wishing to be bound by theory, the increased number of fused mitochondria phenotype in worms fed on Gluconacetobacter spp may explain the increased ATP production phenotype. The mitochondrial fission and fusion dynamics are tightly regulated by drp-1 (Ortholog of human DNML1 [dynamin-related protein]) and fzo-1 (ortholog of human MFN1[Mitofusin]/FZO1GTPase)²⁵. Mutants in fzo-1(tm1133) or drp-1(tm1108) are extremely slow-growing (takes 6 days to reach adulthood from L1-stage) when fed on E. coli OP50 or on Gluconacetobacter spp. Without wishing to be bound by theory, these data indicate that the beneficial effects of Gluconacetobacter spp on mitochondrial function might be via regulation of mitochondrial dynamics.

Since Gluconacetobacter spp feeding induced the expression of peroxisomal biogenesis factors, peroxisomes were examined using a transgenic strain that expresses DAF-22 fusion protein that was tagged with green fluorescent protein (GFP) at its N terminus, under the control of vha-6 intestinal promoter²⁶. In this strain, a punctate signal is observed, which denotes the peroxisomal targeting of the GFP-DAF-22 fusion protein. An increase in the punctate structures was observed in worms fed on Gluconacetobacter spp, indicating an increase in peroxisomes (FIG. 3G). The punctate peroxisomal structures were not observed in worms that were treated with RNAi of prx-5 (ortholog of PXR1 or PEX5 [human receptor for type I peroxisomal targeting signal protein]), which is required for the targeting of GFP-DAF-22 fusion protein to the peroxisomes and fed on either E. coli OP50 or on Gluconacetobacter spp (FIG. 8A). This increase in peroxisomal numbers is specific, changes in the number or morphology of other subcellular structures such as Golgi, gut lysosomal granules, and Endoplasmic reticulum (FIG. 8B-8D) was not observed. Since peroxisomes are a major endogenous source of hydrogen peroxide (H₂O₂), it was examined whether Gluconacetobacter spp feeding increases H₂O₂. To measure endogenous H₂O₂ levels, transgenic jrIs1[Prpl-17::HyPer] worms expressing HyPer sensor²⁷ were fed on Gluconacetobacter spp and E. coli OP50. Compared to the worms fed on E. coli OP50, worms fed on Gluconacetobacter spp had slightly lower levels of H₂O₂ indicating that Gluconacetobacter spp does not increase endogenous H₂O₂ production (FIG. 3H). Even in HyPer sensor worms fed on Gluconacetobacter spp and treated with H₂O₂ had slightly lower level of H₂O₂ levels compared to the worms fed on E. coli OP50 (FIG. 3H) indicating an increased efficiency of H₂O₂ detoxification. Consistent with this observation, worms fed on Gluconacetobacter spp and treated with H₂O₂ had slightly lower levels of H₂O₂ compared to the worms fed on E. coli OP50 as assessed using the Amplex red assay (FIG. 8E). One of the major ways in which organisms handle ROS such as H₂O₂ is through glutathione oxidation²⁷. Using a transgenic worm strain that expresses Grx1-roGFP2, which is a ratiometric biosensor that detects glutathione redox potential²⁷, it was found that the glutathione intracellular concentrations were not affected in worms fed on Gluconacetobacter spp compared to worms fed on E. coli OP50 (FIG. 8F). Without wishing to be bound by theory, it is possible that worms fed on Gluconacetobacter spp have higher levels of peroxisomal catalases, which detoxifies H₂O₂.

Aging-related changes in mitochondria are associated with decline in mitochondrial activity²⁸. In aging animals, impairment of mitochondrial function such as decreased oxidative capacity, decreased ATP production, reduced oxidative phosphorylation, and increased ROS production are observed²⁹. Age-dependent decline in ATP production, metabolism, mitochondrial content and function were observed in C. elegans ^(30,31). The effect of Gluconacetobacter spp feeding on mitochondrial function was assessed in aging worms. It was found that in worms fed on E. coli OP50, ATP levels decrease significantly as the worms age (FIG. 4A). However, worms fed on Gluconacetobacter spp had significantly higher ATP content compared to worms fed on E. coli OP50 even as the worms age (FIG. 4A). The effects of Gluconacetobacter spp feeding is dominant because mixture of Gluconacetobacter spp with E. coli OP50 was sufficient to induce increased ATP production (FIG. 4B).

To test whether the phenotypes associated with Gluconacetobacter spp feeding are strain-specific, the ATP production was assessed in response to other Gluconacetobacter strains. It was found that other Gluconacetobacter strains including Gluconacetobacter hansenii (MGH isolate), the canonical Gluconacetobacter hanseni ATCC 23769, and non-cellulose producing mutant of G. hanseni ATCC 23769 each induced increased ATP production compared worms fed on E. coli OP50 (FIG. 4C).

Further, a variety of Gluconobacter and Acetobacter strains were isolated from rotting apples and grapes, by selecting for bacteria that produce acids and form a characteristic clear halo around media plates containing CaCO₃ ⁷ (FIG. 8G). All these microbes were able to induce increased ATP production compared to worms fed on E. coli OP50 (FIG. 4D) except for G. kondanii and G. frateuri, which were pathogenic to C. elegans (FIG. 4D).

One of the key questions that the inventors wanted to answer was how Gluconacetobacter spp feeding suppresses defects associated with mitochondrial mutants. To address this question, a forward genetic transposon screen for mutant microbial strains that failed to suppress the developmental growth phenotype of spg-7(ad2249) mutants was conducted. Since the Gluconacetobacter spp are very slow growing, the mutant screen was conducted on Gluconobacter oxydans. ˜2000 G. oxydans transposon mutants were isolated and fed individually to synchronized L1-stage spg-7(ad2249) mutants. After 3 days of incubation, the worms were scored for percent of worms that reached L4-stage or adulthood. In this screen, 11 mutants were identified that failed to suppress the slow developmental growth phenotype of spg-7(ad2249) mutants (FIGS. 8H-8I). Further, these 11 mutants failed to accelerate the developmental growth rate of wildtype worms (FIG. 9A). In addition, in worms fed on mutants in membrane-bound PQQ-dependent glucose dehydrogenase (GOX0265; mGDH), Cytochrome o ubiquinol oxidase subunit II (GOX1911), and ubiquinol-cytochrome c reductase iron-sulfur subunit, the ATP production was decreased compared to worms fed on Wildtype G. oxydans (FIG. 4E). However, in the worms fed on mutants in Carbon-Nitrogen hydrolase and TonB-dependent outer membrane receptor protein, the ATP levels were similar to the worms fed on Wildtype G. oxydans (FIG. 4E).

It was next tested whether the G. oxydans mutants affect the ability to produce acids using the CaCO₃ clearance assay. It was found that mutants in membrane-bound PQQ-dependent glucose dehydrogenase (GOX0265; mGDH), Cytochrome o ubiquinol oxidase subunit II (GOX1911), ubiquinol-cytochrome c reductase iron-sulfur subunit, and Carbon-Nitrogen hydrolase fail to form a clear halo around media plates containing CaCO₃ (FIG. 5B).

Six independent alleles of a gene encoding for Membrane-bound PQQ-dependent glucose dehydrogenase (Table 2), which oxidizes D-glucose to D-gluconate that can be further oxidized to two different keto-D-gluconates, 2-keto-D-gluconate and 5-keto-D-gluconate, as well as 2,5-di-keto-D-gluconate^(32,33) were isolated.

TABLE 2 Alleles Membrane bound glucose dehydrogenase 6 Cytochrome o ubiquinol oxidase 1 Ubiquinol-cytochrome C reductase iron-sulfur subunit 1 tonB-dependent receptor protein 2 Carbon nitrogen hydrolase 1

An independent deletion mutation in glucose dehydrogenase of G. oxydans isolated by another lab³⁴ also failed to suppress the slow developmental growth phenotype of spg-7(ad2249) mutants (FIG. 9C).

One of the characteristic attributes of acetic acid bacteria, including G. oxydans, is their ability to incompletely oxidize a variety of substrates including sugars³³. This incomplete oxidation is catalyzed by various membrane-bound dehydrogenases including Membrane-bound PQQ-dependent glucose dehydrogenase³⁴. Independent deletion alleles in various dehydrogenases were tested and it was found that spg-7(ad2249) mutant worms fed on deletion mutations in Membrane-bound PQQ-dependent glucose dehydrogenase, FAD-dependent Membrane-bound dehydrogenase, and Membrane-bound PQQ-dependent dehydrogenase 3 grew slower compared to worms fed on wildtype G. oxydans (FIG. 9C). FAD-dependent membrane-bound dehydrogenase is the D-gluconate-2-dehydrogenase, which oxidizes D-gluconate to 2-keto-gluconate³⁴. The function of Membrane-bound PQQ-dependent dehydrogenase 3 is not known. Further, it was found that ATP production was decreased in worms fed on deletion mutations in Membrane-bound PQQ-dependent glucose dehydrogenase, FAD-dependent Membrane-bound dehydrogenase, and Membrane-bound PQQ-dependent dehydrogenase 3 compared to worms fed on wildtype G. oxydans (FIG. 4F).

To determine whether Gluconacetobacter spp has similar biological effects in humans, human primary dermal fibroblasts were exposed to Gluconacetobacter spp and E. coli OP50. Exposure of E. coli OP50 to human primary dermal fibroblasts results in significant reduction in the ATP production while Gluconacetobacter spp does not affect ATP production compared to the mock-treated cells (FIG. 9D-9E). Since ATP levels are an indicator of metabolically active cells, which is a measure of cellular viability, the reduction of ATP levels in cells exposed to E. coli OP50 is an indicator of cell death or reduced viability. Without wishing to be bound by theory, the reduced viability may be a result of infection. Interestingly, Gluconacetobacter spp does not reduce the cellular ATP production even at higher doses of the bacteria (Fig. S5E) indicating that Gluconacetobacter spp is not toxic or pathogenic to cells. PGC-1a (Peroxisome proliferator-activated receptor gamma coactivator 1-alpha) is the master regulator of mitochondrial biogenesis and it regulates several genes involved in energy metabolism by its interaction with the nuclear hormone receptor, PPAR alpha³⁵. Using RT-QPCR, it was found that PGC-1α gene expression was increased in human primary dermal fibroblasts exposed to Gluconacetobacter spp compared to mock-treated cells (FIG. 4H). PGC-1α induces the transcription of nuclear respiratory factor 1, leading to the increased expression of mitochondrial transcription factor A (TFAM)^(36,37). TFAM is the master regulator of mitochondrial phosphorylative oxidation (mOXPHOS) required for mitochondrial transcription and mitochondrial genome replication³⁸. Using RT-QPCR, it was found that TFAM gene expression was increased in human primary dermal fibroblasts exposed to Gluconacetobacter spp compared to mock-treated cells (FIG. 4H). Since TFAM induces the mitochondrial DNA replication, QPCR for mitochondrial DNA copy numbers (mtDNA) was conducted. It was found that the mtDNA copy numbers were increased in human primary dermal fibroblasts exposed to Gluconacetobacter spp compared to mock-treated cells (FIG. 4I). An increase in the PGC-1α and TFAM expression, and mtDNA copy number reveals an overall enhancement of mitochondrial activity.

References for Example 1

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A mutation in succinate dehydrogenase     cytochrome b causes oxidative stress and ageing in nematodes. Nature     394, 694-697 (1998). -   12. Feng, J., Bussière, F. & Hekimi, S. Mitochondrial electron     transport is a key determinant of life span in Caenorhabditis     elegans. Dev. Cell 1, 633-644 (2001). -   13. Lagido, C., McLaggan, D. & Glover, L. A. A Screenable In Vivo     Assay for Mitochondrial Modulators Using Transgenic Bioluminescent     Caenorhabditis elegans. J Vis Exp e53083-e53083 (2015).     doi:10.3791/53083 -   14. Haynes, C. M. & Ron, D. The mitochondrial UPR-protecting     organelle protein homeostasis. J. Cell. Sci. (2010). -   15. Pellegrino, M. W., Fiorese, C. J., Baker, B. M. & Haynes, C. M.     Mitochondrial import efficiency of ATFS-1 regulates mitochondrial     UPR activation. Science (2012). -   16. Munkacsy, E. et al. DLK-1, SEK-3 and PMK-3 Are Required for the     Life Extension Induced by Mitochondrial Bioenergetic Disruption     in C. elegans. PLoS Genet 12, e1006133 (2016). -   17. Erkut, C., Gade, V. R., Laxman, S. & Kurzchalia, T. V. The     glyoxylate shunt is essential for desiccation tolerance in C.     elegans and budding yeast. Elife 5, 12897 (2016). -   18. Amrit, F. R. G. et al. DAF-16 and TCER-1 Facilitate Adaptation     to Germline Loss by Restoring Lipid Homeostasis and Repressing     Reproductive Physiology in C. elegans. PLoS Genet 12, e1005788     (2016). -   19. Ratnappan, R. et al. Germline signals deploy NHR-49 to modulate     fatty-acid β-oxidation and desaturation in somatic tissues of C.     elegans. PLoS Genet 10, el004829 (2014). -   20. Van Gilst, M. R., Hadjivassiliou, H., Jolly, A. &     Yamamoto, K. R. Nuclear hormone receptor NHR-49 controls fat     consumption and fatty acid composition in C. elegans. PLoS Biol 3,     e53 (2005). -   21. Lee, K., Goh, G. Y. S., Wong, M. A., Klassen, T. L. &     Taubert, S. Gain-of-Function Alleles in Caenorhabditis elegans     Nuclear Hormone Receptor nhr-49 Are Functionally Distinct. PLoS ONE     11, e0162708 (2016). -   22. Sapir, A. et al. Controlled sumoylation of the mevalonate     pathway enzyme HMGS-1 regulates metabolism during aging. Proc Natl     Acad Sci USA 111, E3880-9 (2014). -   23. Tondera, D. et al. SLP-2 is required for stress-induced     mitochondrial hyperfusion. EMBO J 28, 1589-1600 (2009). -   24. Babbar, M. & Sheikh, M. S. Metabolic Stress and Disorders     Related to Alterations in Mitochondrial Fission or Fusion. Mol Cell     Pharmacol 5, 109-133 (2013). -   25. Rolland, S. G., Lu, Y., David, C. N. & Conradt, B. The     BCL-2-like protein CED-9 of C. elegans promotes FZO-1/Mfn1,2- and     EAT-3/Opal-dependent mitochondrial fusion. J. Cell Biol. 186,     525-540 (2009). -   26. Zhang, S. O. et al. Genetic and dietary regulation of lipid     droplet expansion in Caenorhabditis elegans. Proc Natl Acad Sci USA     107, 4640-4645 (2010). -   27. Back, P. et al. Exploring real-time in vivo redox biology of     developing and aging Caenorhabditis elegans. Free Radic. Biol. Med.     52, 850-859 (2012). -   28. Haigis, M. C. & Yankner, B. A. The aging stress response. Mol.     Cell 40, 333-344 (2010). -   29. Balaban, R. S., Nemoto, S. & Finkel, T. Mitochondria, oxidants,     and aging. Cell 120, 483-495 (2005). -   30. Brys, K., Castelein, N., Matthijssens, F., Vanfleteren, J. R. &     Braeckman, B. P. Disruption of insulin signalling preserves     bioenergetic competence of mitochondria in ageing Caenorhabditis     elegans. BMC Biol. 8, 91 (2010). -   31. Gruber, J. et al. Mitochondrial changes in ageing Caenorhabditis     elegans—what do we learn from superoxide dismutase knockouts? PLoS     ONE 6, el9444 (2011). -   32. Matsushita, K., Toyama, H. & Adachi, O. Respiratory chains and     bioenergetics of acetic acid bacteria. Adv. Microb. Physiol. 36,     247-301 (1994). -   33. Saichana, N., Matsushita, K., Adachi, O., Frébort, I. &     Frebortova, J. Acetic acid bacteria: A group of bacteria with     versatile biotechnological applications. Biotechnol. Adv. 33,     1260-1271 (2015). -   34. Peters, B. et al. Characterization of membrane-bound     dehydrogenases from Gluconobacter oxydans 621H via whole-cell     activity assays using multideletion strains. Appl. Microbiol.     Biotechnol. 97, 6397-6412 (2013). -   35. Lin, J., Handschin, C. & Spiegelman, B. M. Metabolic control     through the PGC-1 family of transcription coactivators. Cell Metab.     1, 361-370 (2005). -   36. Scarpulla, R. C. Metabolic control of mitochondrial biogenesis     through the PGC-1 family regulatory network. Biochim. Biophys. Acta     1813, 1269-1278 (2011). -   37. Goffart, S. & Wiesner, R. J. Regulation and Co-Ordination of     Nuclear Gene Expression During Mitochondrial Biogenesis.     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Example 2: Materials and Methods

Caenorhabditis elegans strains were maintained on NGM plates and OP50 Escherichia coli bacteria at 20° C. as described¹. The wild-type strain was N2 Bristol. The strains used are described in Table 3.

TABLE 3 Strain Name Description SAL150 denEx28 [F10A3.4::GFP + pha-1(+)] SAL146 denEx24 [clec-85p::GFP + pha-1(+)] SAL144 denEx22 [K08D8.5::GFP + pha-1(+)] SAL143 denEx21 [F55G11.7::GFP + pha-1(+)] SAL139 denEx17 [dod-22::GFP + pha-1(+)] SAL129 denEx14 [lys-1::GFP + pha-1(+)] SAL117 denEx11 [spp-7::GFP + pha-1(+)] SAL109 denEx6 [abf-3::GFP + pha-1(+)] SAL107 denEx4 [abf-1::GFP + pha-1(+)] SAL105 denEx2 [lys-7::GFP + pha-1(+)] AY101 acls101 [F35E12.5p::GFP + rol-6(su1006)] SAL148 denEx26 [F08G5.6::GFP + pha-1(+)] BC14852 sEx14852[rCesF15B9.1::GFP + pCeh36] DM7065 raEx65 [C53B4.3::GFP + pha-1(+) + rol-6]. BC15698 sEx15698 [rCes K02G10.3::GFP + pCeh36] BC11949 sEx11949 [rCes C01H6.4::GFP + pCeh36] BC16086 sEx16086 [rCes F08F8.3a::GFP + pCeh36] CF2222 muEx336 [mtl-1::RFP + rol-6(su1006)] BC15536 sEx15536 [rCes T19B10.1::GFP + pCeh36] BC14979 sEx14979 [rCesF57B10.9::GFP + pCeh36]. SD1631 ccls4251 [(pSAK2) myo-3p::GFP::LacZ::NLS + (pSAK4) myo-3p::mitochondrial GFP + dpy-20(+)] I. stls10656 [nhr-69p::HIS-24::mCherry + unc-119(+)]. VS11 hjls73 [vha-6p::GFP::daf-22 + C. briggsae unc-119(+)]. RW11514 stls11514 [nhr-64::H1-wCherry + unc-119(+)]. BC14632 sEx14632 [rCes F59F4.1::GFP + pCeh361] BC14386 sEx14386 [rCes T14D7.1::GFP + pCeh361]. BC11106 sEx11106 [rCes Y50D7A.7::GFP + pCeh361]. BC11207 sls10648 [rCes Y45F3A.3::GFP + pCeh36]. VL714 wwEx53 [acdh-2p::GFP]. VL717 wwEx54 [acdh-1p::GFP]. BC11314 sEx11314 [rCesT20G5.2::GFP + pCeh36] AGD418 uthls205 [crtc-1p::crtc-1::RFP::unc-54 3′UTR + rol- 6(su1006)] BC10214 sEx10214 [rCes ZK1248.14::GFP + pCeh36] XA6900 qaEx6900 [ftn-1p::pes-10::GFP-his + pha-1(+)]. XA6901 qaEx6901 [ftn-2p::pes-10::GFP::his + lin-15(+)]. BC10060 sEx884 [rCesC12C8.1::GFP + pCeh36] BC14666 sEx14666 [rCesF54F3.3::GFP + pCeh36] PP563 unc-119(ed4)III; hhls64 [unc-119(+); sur-5::UbV-GFP]III DA2123 adls2122 [lgg-1p::GFP::lgg-1 + rol-6(su1006)] icl-1::gfp BC10434 sEx10434 [rCes Y46G5A.17::GFP + pCeh361] BC14873 sEx14873 [rCes F39G3.7::GFP + pCeh361]. BC12611 sls11096 [rCes T25G12.5::GFP + pCeh361] BC15507 sEx15507 [rCesT08B2.7b::GFP + pCeh361] BC14661 sEx14661[rCes F08A8.2::GFP + pCeh361]. BC11281 sEx11281 [rCes R07H5.2::GFP + pCeh361] BC14848 sEx14848 [rCesC47B2.8::GFP + pCeh361] BC12923 sls12801 [rCes B0303.3::GFP + pCeh361] BC14789 sEx14789 [rCes Y38F1A.6::GFP + pCeh361] tbb-6::gfp BC15777 sEx15777 [rCesF10D2.9::GFP + pCeh361] GR2183 mgls72 [rpt-3p::GFP + dpy-5(+)] II. RW10592 zuls178 [his-72(1kb 5′ UTR)::his-72::SRPVAT::GFP::his- 72 (1KB 3′ UTR) + 5.7 kb Xbal - HindIII unc-119(+)]. stls10024 [pie-1::H2B::GFP::pie-1 3′ UTR + unc-119(+)]. stls10520 [nhr-57::H1-wCherry + unc-119(+)]. CL2070 dvls70 [hsp-16.2p::GFP + rol-6(su1006)]. AU133 agls17 [myo-2p::mCherry + irg-1p::GFP] IV. clec-60::gfp IG274 frls7 [nlp-29p::GFP + col-12p::DsRed] IV. SJ4100 zcls13[hsp-6::GFP]. SJ4005 zcls4 [hsp-4::GFP] V SJ4058 zcls9 [hsp-60::GFP + lin-15(+)]. LD1171 ldls3 [gcs-1p::GFP + rol-6(su1006)]. CL2166 dvls19 [(pAF15)gst-4p::GFP::NLS] III. CF1553 muls84 [(pAD76) sod-3p::GFP + rol-6(su1006)]. JG1 ajls1(pgp-5::gfp) BC15680 sEx15680 [rCesC47A10.1::GFP + pCeh361] SD1448 gals240 [ugt-22p::his-24::mCherry + unc-119(+)] SD1444 gals237 [cyp-25A2p::his-24::mCherry + unc-119(+)]. BC10034 sEx868 [rCesT21E8.1::GFP + pCeh361] BC13865 sEx13865 [rCesY17G9B.3::GFP + pCeh361]. BC14956 sEx14956 [rCesF42E11.1::GFP + pCeh361] JG4 cyp-13A7::GFP BC15565 sEx15565 [rCesH23N18.3::GFP + pCeh361] BC14926 sEx14926 [rCesK09A11.4::GFP + pCeh361] BC13846 sEx13846 [rCesB0213.15::GFP + pCeh361] BC14562 sEx14562[rCesT11F9.11::GFP + pCeh361] BC15044 sEx15044 [rCes F01D5.9::GFP + pCeh361] BC10338 sls10109 [rCesY32H12A.3::GFP + pCeh361] BC10672 sls10263[rCesF35H8.6::GFP + pCeh361]. BC10366 sEx10366 [rCes T02D1.5::GFP + pCeh361] BC10058 sEx10058 [rCes C56E6.5::GFP + pCeh36[ BC12028 sEx12028 [rCesF57C12.4::GFP + pCeh361] BC10257 sEx10257 [rCesZK455.7::GFP + pCeh361] BC11571 sEx11571 contains [rCes F39G3.1::GFP + pCeh36] BC10027 sEx861 [rCes Y50E8A.16::GFP + pCeh361]. CY573 bvls5 [cyp-35B1p::GFP + gcy-7p::GFP] STE68 nhr-49(nr2041) I WBM409 nhr-49(nr2041) I; wbmEx149[ges-1p::3xHA::nhr- 49(cDNA)::unc-54 3′UTR + myo-3p::mCherry::unc-54 3′UTR]. MH5239 prx-5(ku517) II CF2167 tcer-1(tm1452) II CF2031 muEx306 [tcer-1::GFP + odr-1::RFP] DA2249 spg-7(ad2249) I QC134 nduf-7(et19) I CW152 gas-1(fc21) X TK22 mev-1(knl) III MQ887 isp-1(qm150) IV PE254 fels4 [sur-5p::luciferase::GFP + rol-6(su1006)] V PS6187 pha-1(e2123) unc-119(ed4) III; syEx1155 [myo- 3p::tomm-20::mRFP::3xMyc + Cbr-unc-119(+)] VS11 hjls73 [vha-6p::GFP::daf-22 + C. briggsae unc-119(+)] VS8 dhs-28(hj8) X VS17 hjls9 [ges-1p::glo-1::GFP + unc-119(+)] VS25 hjls14 [vha-6p::GFP::C34B2.10(SP12) + unc-119(+)] JV1 unc-119(ed3) III; jrls1 [rpl-17p::HyPer + unc-119(+)]. JV2 unc-119(ed3) III; jrls2 [rpl-17p::Grx1-roGFP2 + unc- 119(+)]

E. coli OP50, Gluconobacter oxydans DSM 2343 (621H) and its mutant derivatives were cultivated in a medium containing LB medium containing 1% glucose. The cultures were centrifuged and seeded onto NGM media without any antibiotics.

Gluconacetobacter strains were routinely grown in standard Hestrin-Schramm agar (D-glucose 20 g/L, yeast extract 5 g/L, peptone 5 g/L, disodium phosphate 2.7 g/L, citric acid 1.15 g/L, and agar 15 g/L) and incubated for 4 days at 30° C. For liquid culture, agar in the media was omitted. E. coli OP50 was also grown in the same media at 30° C. The liquid cultures were spotted onto NGM media plates without any antibiotics and left to grow at room temperature for at least 3 days.

Screening for Transcription Factors Responsible for Induction of Metabolic Genes in Response to Gluconoacetobacter Spp

To identify the transcription factor(s) that mediate the induction of metabolic genes in response to Gluconacetobacter feeding, the inventors conducted a cherry-picked RNAi screen of genes that were previously implicated in metabolism²⁻¹³.

Feeding RNAi clones corresponding to dsRNA-control, daf-16, pha-4, hlh-30, skn-1, hsf-1, daf-12, nhr-80, nhr-49, tcer-1, sbp-1, nhr-69, and nhr-64 were grown in LB media with 25 μg/ml carbenicillin overnight and seeded onto RNAi agar plates containing 1 mM IPTG. The plates were dried in a laminar flow hood and incubated at room temperature overnight to induce dsRNA expression. 200 synchronized L1 larvae each of pmp-4::gfp, cpt-2::gfp, ech-1.2::gfp, acox-1.2::gfp, acdh-7::gfp, and prx-6::gfp expressing animals were placed onto each of the RNAi-containing agar plates, allowed to develop at 20° C. for 4 days. When the animals reached adult-stage, the worms were bleach-prepped. 20 synchronized L1 larvae were then placed on Gluconacetobacter seeded plates and scored for failure to induce GFP expression. dsRNA-control RNAi treated worms fed on Gluconacetobacter-seeded plates were used as controls.

Screening for Microbes that Suppress the Slow Developmental Growth Rate Phenotype of spg-7(ad2249) Mutants

˜200 Microbial strains were grown individually and seeded onto NGM media plates. ˜20 Synchronized L1-stage spg-7(ad2249) mutant animals were placed on the 24-well plates and visually screened at 60 hours for the wells that contained animals that were fast growing compared to the worms fed on E. coli OP50. 6 microbial strains were recovered in the screen.

Isolation of G. oxydans Tn5 Transposon Mutants

Tn5 transposon mutagenesis in G. oxydans was performed using vector pME9978 obtained from Prof. Stephan Heeb, University of Nottingham, UK. pME9978 was transformed into E. coli S17-1 and selected on gentamicin and ampicillin LB media plates. pME9978 present in E. coli S17-1 cells were transferred into G. oxydans through conjugation. Conjugation was performed by mixing E. coli S17-1 bearing pME9978 and G. oxydans in suspension, plating them on LB medium, and incubating at 30° C. for 4 hours. The culture was scrapped from the LB plate and resuspended in 10 ml of M9 buffer. The resultant cell suspension was serially diluted up to 10⁻⁶ and plated out on the selection media plates (LB media containing 1% glucose, 10 μg/ml-1 gentamicin, and 50 μg ml-1 cefoxitin). G. oxydans is naturally resistant cefoxitin while E. coli S17-1 is sensitive. Gentamicin-resistant G. oxydans colonies appeared after 4 days of incubation at 30° C. 2000 of these colonies were picked onto 96-well blocks filled with liquid selection media (LB media containing 1% glucose, 10 μg/ml-1 gentamicin, and 50 μg ml-1 cefoxitin), grown at 30° C. for 2 days and stored at −80° C.

Screening for G. oxydans Mutants that Failed to Suppress the Slow Developmental Growth Rate Phenotype of spg-7(ad2249) Mutants

G. oxydans Tn5 mutants were grown in LB liquid media containing 1% glucose, 10 μg/ml⁻¹ gentamicin, and 50 μg ml⁻¹ cefoxitin and spotted onto 24-well NGM media plates. ˜20 Synchronized L1-stage spg-7(ad2249) mutant animals were placed on the 24-well plates and visually screened at 60 hours for the wells that contained animals that were slow-growing compared to the worms fed on wildtype G. oxydans. 11 mutants were recovered in the screen.

Identification of Transposon Insertion Sites in the G. oxydans Tn5 Mutants

The transposon mutant bacteria were grown in 100 ml of LB liquid media containing 1% glucose, 10 μg/ml-1 gentamicin, and 50 μg ml-1 cefoxitin and centrifuged at 2500 g for 15 minutes. Genomic DNA isolation was performed using a commercial genomic DNA isolation kit (Qiagen). The isolated genomic DNA was subjected to restriction digestion using NcoI (does not cut pME9978 plasmid) and heat-inactivated. The restriction fragments were self-ligated with T4 DNA ligase and electroporated into pir E. coli strain and selected on gentamicin containing LB media plates at 37° C. overnight. Since the transposon contains R6Kγori origin of replication, it can grow as independent plasmid in the pir E. coli strain. Multiple colonies from the gentamicin plates were pooled together and grown in gentamicin containing LB media plates at 37° C. overnight. The cultures were centrifuged and plasmid isolation was performed. The plasmid was sequenced to find the transposon insertion site using the following primers:

tpnRL17 (SEQ ID NO: 11): 5′-AACAAGCCAGGGATGTAACG-3′ tpnRL13 (SEQ ID NO: 12): 5′-CAGCAACACCTTCTTCACGA-3′

Transposon Insertion Site in the Mutants

Glucose dehydrogenase_G7 (SEQ ID NO: 13): CAGCTGACGCTTCGTCCGAAGAACCCGCTCTCCGATGCCGATATCTGGGGTGGCACAATC...Tn5...GGC ACAATCTTCGACCAGATGTTCTGCAGCATCTACTTCCACTCCCTGCGCTACGAAGGT Glucose dehydrogenase_G9 (SEQ ID NO: 14): CTACATCCCGACCAAGACGGGCGATATCTTTGTCCTCGACCGCCGTACGGGCAAGGAAG...Tn5...GGG CAAGGAAGTCGTCGCTGCTCCTGAAACACCAGTTCCAGGTGGTGCAGCTCCGGGCGA Cytochrome 0 Ubiquinol oxidase subunit_G1 (SEQ ID NO: 15): AGCACCCACGCCTACGACCCGTACCGCCCCCTTCAGACGGCTGACAACGTCAAGCCCTG...Tn5...GACA GCGTCAAGCCACTGAATGTTCAGGTGGTCTCTCTCGACTGGAAATGGCTGTTCATC Glucose dehydrogenase_G6 (SEQ ID NO: 16): CGCACCAACAAGGTGGTCTGGCAGCATCGTAACGGTACGCTCCGTGACTCCATGCACGGC...Tn5...ATG CACGGCAGCTCCCTGCCCATCCCGCTGCCTCCGATCAAGATCGGTGTTCCGAGCCTT tonB_G2 (SEQ ID NO: 17): TACAAGTGGTATCGATTGGGATTTTGATTATCGGATCCGTCTGACTAGCATGGATTCCAT...Tn5...GGA TTCCATCACTGTCAGCAATAACCTGCAGAACCTGGTCAATTTTTCCCAGCAGCAGAC Ubiquinol-cytochrome C reductase iron-sulfur subunit_G3 (SEQ ID NO: 18): CATCGGCGTCATGATCGGGATCTGCACGCATCTGGGC...Tn5...TGCGTGCCGACTTTCGACGCCCCGAC GCAGGCAGAACCTGCCGGGAA Glucose dehydrogenase_G14 (SEQ ID NO: 19): CGATGCAGAAACCGGGCAGAAGTGTTCCGGCTTTGGCAACGACGGCGAACTGGAACCTG...Tn5...GAA CTGGAACTGCGCGAGCCGAACCAGCCTTACGTCACGCCAGGCATGTATGAGCCGACG Glucose dehydrogenase_promoter_G15 (SEQ ID NO: 20): TCTTAATGCGCTTCTATGTGTTTGTCCGAAGGTCAAGTGC...Tn5...AGGTCAAGTGCTGCACCAAATAA CAGCTCTAGGAACATCATGAGCACATCTTCCCGGC tonB_G11 (SEQ ID NO: 21): GCAGTAATTTCGTGTCTGCTTCCTCCAGTCAGGTTCCGACCCTGTTT....Tn5...GGTGGTAATACAAAGC TGCGTCCAGAAGCAGGGCGTACCTACACCTTTGGT Glucose dehydrogenase_G13 (SEQ ID NO: 22): TGGCGATCGCTGGTCTCCGCTGAAGCAGATCAATTCGACCAATGTTCAGAACCTCAAGGT...Tn5...CCT CAAGGTGGCATGGCACATCCACACCAAGGATCTGATGGGACCGAATGATCCGGGCGA Carbon-Nitrogen Hydrolase_G5 (SEQ ID NO: 23): AGACTCAATAGCGCGAGCACGGACAAGAATGTCCCAGTGAGCTTCACCCGTTTGCTGCGT...Tn5...AAA CGCTGCGGGCAGAACAATCATCTCAACATCCGCAGCCCGAAG Isolation of Acetobacteraceae from Fruits

Members of the Acetobacteraceae family are characterized by acid production resulting in clearing of CaCO₃ and formation of halo around the colonies on calcium carbonate-containing media². Samples of rotting apples, grapes, and oranges were crushed aseptically and mixed with 9 ml of M9 buffer and serially diluted up to 10⁻⁶ dilution. 100 μl of dilutions were spread on CaCO₃ medium (8% Glucose, 0.5% Yeast extract, 0.2% Mannitol, 0.05% Magnesium Sulphate, 10% Calcium carbonate, 100 μg/ml Cycloheximide, 10 μg/ml Nystatin).

Plates were incubated under aerobic conditions at 30° C. for 3-4 days. Colonies showing a clear halo were selected. Colony PCRs were conducted using the following primers:

27F (SEQ ID NO: 24): AGAGTTTGATCMTGGCTCAG 1492R (SEQ ID NO: 25): TACGGYTACCTTGTTACGACTT

The conditions used for touchdown colony PCR were as follows: 95° C. for 10 minutes followed by 15 cycles of 30s at 95° C., 30s at 65° C. (step down of −1° C. for every cycle) and 1 minute at 72° C. This was followed by 40 cycles of 30s at 95° C., 30s at 50° C. and 1:30 minutes at 72° C.

16S rRNA sequencing on the isolates were conducted for identification of the isolates.

Microscopy

For high-magnification differential interference contrast and fluorescence images, worms treated with appropriate conditions were mounted onto agar pads and images were acquired using a Zeiss AXIO™ Imager Z1 microscope fitted with a Zeiss AxioCam™ HRc camera and Axiovision™ software. Fluorescent images were converted to 16-bit images, thresholded and quantified using ImageJ. Student's t test was used determine statistical significance. GraphPad™ Prism 8.0 was used for these calculations and generating graphs. Low-magnification bright-field images were acquired using a Zeiss AxioZoom™ V16 Microscope, equipped with a Hammamatsu Orca™ flash 4.0 digital camera, and using Axiovision™ software. Immunofluorescence images (shown in FIG. 2) were acquired with an IX-70 microscope (Olympus, Waltham, Mass.) fitted with a cooled CCD camera (CH350; Roper Scientific) driven by the Delta Vision system (Applied Precision, Pittsburgh, Pa.). Images were deconvolved using the SoftWoRx 3.3.6 software (Applied Precision).

Measuring Endogenous Hydrogen Peroxide Levels Using HyPer Strain

To measure endogenous hydrogen peroxide levels, transgenic jrIs1 [Prpl-17::HyPer] worms expressing a HyPer as described3 was used. Synchronized L1-stage transgenic jrIs1[Prpl-17::HyPer] animals were grown in E. coli OP50 and G. hansenii and about 1000 L4-stage worms were harvested in 96 microtiter well plates. For H₂O₂ treatment experiment, H₂O₂ was added to the worms in the 96-well itself and measurements were taken within 15 minutes. An excitation wavelength of either 490 nm or 405 nm was used to measure oxidized or reduced HyPer™ probe fluorescence respectively with an emission filter of 535 nm. The absorbance at 620 nm was used to normalize for worm numbers. The statistical significance of differences between conditions was determined by using unpaired t-test. GraphPad™ Prism 8.0 was used for these calculations.

Measuring Endogenous GSSG/2GSH Ratios

To measure in vivo GSSG/2GSH ratios, transgenic jrIs2[Prpl-17::Grx1-roGFP2] worms expressing a Grx1-roGFP2 as described³ were used. Synchronized L1-stage transgenic jrIs2[Prpl-17::Grx1-roGFP2] animals were grown in E. coli OP50 and G. hansenii and about 1000 L4-stage worms were harvested in 96 microtiter well plates after washing at least six times in M9 buffer. For H₂O₂ treatment experiment, H₂O₂ was added to the worms in the 96-well itself and measurements were taken within 15 minutes. An excitation wavelength of either 490 nm or 405 nm was used to measure reduced or oxidized Grx1-roGFP2 probe fluorescence respectively with an emission filter of 535 nm. The absorbance at 620 nm was used to normalize for worm numbers. The statistical significance of differences between conditions was determined by using unpaired t-test. GraphPad™ Prism 8.0 was used for these calculations.

Measuring Endogenous Hydrogen Peroxide Levels Using Amplex™ Red Assay

Measuring endogenous hydrogen peroxide levels using Amplex™ Red assay was performed as described⁴.

To measure ROS production, synchronized L1-stage wildtype worms were grown in E. coli OP50 and G. hansenii and about 1000 L4-stage worms were harvested in 96 microtiter well plates after washing at least six times in M9 buffer, followed by 3 washes with the reaction buffer supplied with the Amplex™ Red Hydrogen Peroxide/Peroxidase assay kit. Equal volume of the Amplex™ Red reaction buffer was then added to the wells, the absorbance at 540 nm was read after 3 hours with a plate reader (SpectraMax™ plate reader). For H₂O₂ treatment experiment, H₂O₂ was added to the worms in the 96-well itself and measurements were taken after 2 hours. The absorbance at 620 nm was used to normalize for worm numbers. All the values were normalized to the values of control untreated worms. The statistical significance of differences between conditions was determined by using unpaired t-test. GraphPad™ Prism 8.0 was used for these calculations.

Human mtDNA Copy Number Estimation

Human dermal primary Fibroblasts (Coriell GM25438) were grown in 6-well plates with EMEM containing 10% Fetal Bovine Serum, 1% MEM non-essential amino acids, and 1% Penicillin-Streptomycin until the cells were ˜90% confluent in a 37° C., 5% CO₂ humidified incubator. The cells were treated with Mock-treatment or 10⁶ CFU of G. hansenii-treatment for 24 hours and the genomic DNA was isolated using a commercial DNA isolation kit (Qiagen). The quantity and purity of the isolated DNA was assayed using a Nanodrop™ 2000 spectrophotometer (Thermo Scientific, Wilmington, Del., USA) and the samples were stored at −70° C. until use. The relative mtDNA copy number was measured by qPCR as described⁵. The values were normalized to that of a single copy nuclear DNA gene as described. The primer sequences used were:

L394 (SEQ ID NO: 26), 5′-CACCAGCCTAACCAGATTTC-3′ H475 (SEQ ID NO: 27), 5′-GGGTTGTATT-GATGAGATTAGT-3′ HBG1F (SEQ ID NO: 28), 5′-GCTTCTGACACAACTGTGTTCACTAGC-3′ HBG1R (SEQ ID NO: 29) 5′-CACCAACTTCATCCACGTTCACC-3′

L394/H475 were for the mtDNA content, and HBG1F/R primers were for nuclear B-globin gene⁵. qPCR was performed with an iCycler™ machine (Bio-Rad) using iQ SYBR Master Mix (Bio-Rad) and the assays were performed under the following conditions: denaturation at 95° C. for 10 minutes followed by 40 cycles of 10 s at 95° C., 30 at 60° C. and 30s at 72° C. All assays were carried out in triplicate using 10 ng DNA template per reaction. All reactions were performed in triplicate and on 3 biological replicates. The relative mtDNA copy number was calculated using the ΔCt method.

RNA Isolation and Quantitative RT-PCR Analysis of PGC-1 and TFAM

Human primary Fibroblasts were grown in 6-well plates with EMEM containing 10% Fetal Bovine Serum, 1% MEM non-essential amino acids, and 1% Penicillin-Streptomycin until the cells were ˜90% confluent in a 37TMC, 5% CO₂ humidified incubator. The cells were treated with Mock-treated or 10⁶ CFU of G. hansenii-treated for 24 hours. After incubation for 24 h in each condition, total cellular RNA was isolated from cells using commercial RNA isolation kit (Qiagen). Total RNA was DNAase treated using the TURBO DNA-free kit (Applied Biosystems). cDNA was prepared using the First strand cDNA synthesis kit from Invitrogen. qRT-PCR assays were performed under the following conditions: denaturation at 95° C. for 10 minutes followed by 40 cycles of 10 s at 95° C., 30 at 55° C. and 30s at 72° C. The primer sequence used^(6,7):

hTfamF (SEQ ID NO: 30): TGTTCACAATGGATAGGCAC hTfamR (SEQ ID NO: 31): TCTGGGTTTTCCAAAGCAAG hPGC-1αF (SEQ ID NO: 32): TGAAGACGGATTGCCCTCATT hPGC-1αR (SEQ ID NO: 33): GCTGGTGCCAGTAAGAGCTT

All reactions were done in triplicate and on 3 biological replicates. All the values are normalized to the nuclear β-globin gene as internal control as well as to the transcript levels in mock-treated cells.

ATP Determination Assay

ATP determination was performed as described⁸. To measure ATP levels, synchronized L1-stage worms were grown in E. coli OP50 and G. hansenii and were harvested after washing at least six times in M9 buffer and approximately 1000 worms in 100 μl of M9 were frozen in liquid nitrogen and stored at −80° C. until analysis. The samples were placed immediately in boiling water bath for 15 min. After adding twice the amount of distilled water, centrifugation was done at 14,000 rpm for 5 min and supernatant was transferred into a second tube. Equal volume of luciferase reagent (Promega™) was added and luminescence was measured using a plate reader (SpectraMax™ Microplate reader). Protein content was measured using BCA method. ATP concentrations were normalized to protein content of samples. All the values were normalized to wildtype fed on E. coli OP50.

ATP Determination Assay Using the Luciferase Strain

ATP determination assay using the Luciferase strain was described⁹. To measure in vivo ATP production, synchronized L1-stage Psur-5::luc+::gfp worms were grown in E. coli OP50 and G. hansenii and about 1000 adult-stage worms/well were harvested in 96 microtiter well plates after washing at least six times in M9 buffer. 100 μM D-luciferin was added to the wells and the luminescence was measured within 5 min in a SpectraMax™ microplate reader. GFP fluorescence was quantified in SpectraMax™ microplate reader using 485 nm excitation and a 520 nm emission filter. Background measurements were subtracted from readings. Luminescence values were normalized to GFP fluorescence of samples. All the values were normalized to wildtype fed on E. coli OP50. For the RNAi experiments, synchronized L1-stage Psur-5::luc+::gfp worms were grown in E. coli HT115 strain carrying the corresponding the dsRNA until adulthood and egg-prepped. The L1-stage worms were then transferred to either E. coli OP50 or G. hansenii-seeded media plates. For the experiment using rotenone, paraquat, azide, and, antimycin, the worms grown on E. coli OP50 or G. hansenii were washed at least 6 times and transferred to E. coli OP50 plates containing the drugs. The E. coli OP50 plates with proper concentrations of drugs were made one day before use. All the assays were conducted on E. coli OP50 plates to avoid potential drug detoxification by G. hansenii.

Mitotracker CMXRos Staining

For the experiment using Mitotracker™ CMXRos, the worms grown on E. coli OP50 or G. hansenii were washed at least 6 times and transferred to E. coli OP50 plates containing the 10 μM of Mitotracker™ CMXRos. After 24 hours, worms were washed at least 6 times to remove the dye and dropped onto E. coli OP50 plates to clear off non-specific gut staining. After 2 hours, worms were washed at least 6 times and transferred to agar plates for imaging.

Tetramethylrhodamine Ethylester (TMRE) Staining

For the experiment using TMRE, the worms grown on E. coli OP50 or G. hansenii were washed at least 6 times and transferred to E. coli OP50 plates containing the 104 of TMRE. After 24 hours, worms were washed at least 6 times to remove the dye and dropped onto E. coli OP50 plates to clear off non-specific gut staining. After 2 hours, worms were washed at least 6 times and 1000 worms were transferred to each well of 96-well plate and the fluorescence was quantified in SpectraMax™ microplate reader using 549 nm excitation and a 575 nm emission filter.

Optimization of Metabolite Production

It was discovered that when the bacteria are grown in either 0-5% yeast extract broth, the metabolites are not produced. Further, it was found that addition of glucose or other metabolizable monosaccharide sugars such as fructose or disaccharides such as sucrose to the 3% yeast extract medium is required for metabolite production. In addition, it was discovered that as little as 0.5% of such sugars is enough for optimal metabolite production. Thus, it is recommended that any medium used for metabolite production comprise at least 0.5-5% of a metabolizable sugar source.

Further experiments indicate that 3% corn steep liquor is sufficient for optimal metabolite production, thus 0.5-5% corn steep liquor is recommended for optimal production of metabolites. It is contemplated herein that when bacteria are grown on a commercial scale, 3% corn steep liquor may be the preferred method for fermentation.

References for Example 2

-   1. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77,     71-94 (1974). -   2. The Family Acetobacteraceae: The Genera Acetobacter, Acidomonas,     Asaia, Gluconacetobacter, Gluconobacter, and Kozakia.     (Springer-Verlag, 2011). doi:10.1007/SpringerReference_3770 -   3. Back, P. et al. Exploring real-time in vivo redox biology of     developing and aging Caenorhabditis elegans. Free Radic. Biol. Med.     52, 850-859 (2012). -   4. Chavez, V., Mohri-Shiomi, A., Maadani, A., Vega, L. A. &     Garsin, D. A. Oxidative stress enzymes are required for     DAF-16-mediated immunity due to generation of reactive oxygen     species by Caenorhabditis elegans. Genetics 176, 1567-1577 (2007). -   5. Chen, S. et al. Elevated mitochondrial DNA copy number in     peripheral blood cells is associated with childhood autism. BMC     Psychiatry 15, 50 (2015). -   6. Zaccagnino, P. et al. An active mitochondrial biogenesis occurs     during dendritic cell differentiation. Int. J. Biochem. Cell Biol.     44, 1962-1969 (2012). -   7. Oral, E. A. et al. Inhibition of IKKE and TBK1 Improves Glucose     Control in a Subset of Patients with Type 2 Diabetes. Cell Metab.     26, 157-170.e7 (2017). -   8. Palikaras, K. & Tavernarakis, N. Intracellular Assessment of ATP     Levels in Caenorhabditis elegans. Bio Protoc 6, (2016). -   9. Lagido, C., McLaggan, D. & Glover, L. A. A Screenable In Vivo     Assay for Mitochondrial Modulators Using Transgenic Bioluminescent     Caenorhabditis elegans. J Vis Exp e53083-e53083 (2015).     doi:10.3791/53083

Example 3: Treatment of Parkinson's Disease

Parkinson's Disease (PD) is the most common motor-related disorder in middle or late life disease, affecting ˜6.2 million people worldwide.¹ PD is characterized by accumulation of α-synuclein inclusions in the neurons and degeneration and/or loss of dopaminergic neurons. The cardinal clinical symptoms of PD includes slow movement, resting tremor, rigidity, and postural instability.² While a majority of PD cases are of unknown origin and sporadic, mutations in some genes have been associated with rare, familial forms of the disease. Several lines of evidence implicate defects in mitochondrial respiration in the etiology and pathogenesis of PD. First, MPTP, an inhibitor of complex I of the electron transport chain, can induce PD.^(3,4) Inhibition of complex I results in decreased mitochondrial ATP production, increased production of mitochondria-derived Reactive Oxygen Species (ROS), and activation of mitochondria-dependent apoptotic pathways. Second, post mortem studies of PD patients found elevated levels of oxidative stress markers/products⁵⁻⁷ in the dopaminergic neurons. Third, a reduction of mitochondrial complex I activity by 30% was observed in brain as well as peripheral tissues of PD patients.^(8,9) Fourth, neurotoxins such as rotenone, paraquat, and 6-hydroxydopamine (6-OHDA) induce mitochondrial dysfunction resulting in PD-associated phenotypes in animal models.¹⁰ Finally, PD-associated genes such as α-synuclein, LRRK2 (leucine-rich repeat kinase 2), parkin, PINK1, and DJ-1 affect mitochondrial dynamics, trafficking, autophagy, and quality control.^(11,12)

All cells require mitochondria for their energy demands including neurons, which are critically dependent on proper mitochondrial function. Neurons have high metabolic activity and they depend heavily on mitochondria for their bioenergetic demand. Several factors make the neurons in general, and dopaminergic neurons in particular, susceptible to degeneration; these include ROS (which result from dopamine metabolism and mitochondrial dysfunction), low endogenous antioxidant levels, and high levels of iron and calcium (which are known to promote ROS formation).¹³ Further, neuronal tissues contain high levels of polyunsaturated fatty acids, which are prone to lipid peroxidation and the generation of toxic products.¹⁴ Regardless of whether a primary or secondary cause, mitochondrial dysfunction holds promise as a potential therapy target. Aging is the greatest risk factor for PD,¹⁵ thus with increasing average life expectancy worldwide,¹⁶ the number of people affected by PD will rise considerably in the near future. Thus, there is a significant clinical unmet need for new therapeutic approaches that not only can be used for slowing down PD, but also as preventive measures for the aging population.

Mitochondria are highly dynamic organelles required for cellular energy production, response to oxidative stress, and apoptosis. Thus, it is not surprising that mitochondrial dysfunction, characterized by a loss of efficiency in the electron transport chain and reduction in ATP synthesis, is a characteristic of aging, and aging-related neurodegenerative diseases.^(17,18) Despite having distinct pathological and clinical features, several other neurodegenerative disorders including Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis are associated with mitochondrial dysfunction-derived oxidative stress¹⁹ as well; this suggests a common mechanism that contributes to neuronal degeneration²⁰.

While most of the earlier studies on PD focus entirely on the brain pathologies, the gastrointestinal (GI) system is now recognized as an important source for PD pathogenesis.²¹⁻²³ GI symptoms, such as constipation, affects ˜80% of PD-patients and idiopathic constipation is an important risk factor for PD.²⁴ In PD, constipation is associated with alpha-synuclein accumulation in the enteric nervous system,²⁵ gut inflammation, and increased gut permeability.²⁶ Further, the intestinal mucosal inflammation is thought to lead to synuclein accumulation in the enteric nerves, which can then spread in a prion-like fashion to the central nervous system via autonomic connections.²⁷⁻²⁹ Many of the GI tract changes are observed even before the onset of neuronal symptoms;³⁰ thus, PD pathogenesis might act primarily via the GI tract^(31,32).

C. elegans as a model is well-positioned to play an important role in PD-associated discoveries.³³ C. elegans contain well-defined dopaminergic (DA) neurons that are visible under fluorescence microscopy and have a range of locomotor activities.³⁴ All orthologs of genes linked to familial PD are present in C. elegans, except α-synuclein. Ectopic overexpression of α-synuclein produces neurotoxic effects, which can be blocked by neuroprotective genes. A number of worm models of PD have been generated through either exposing worms to neurotoxins such as MPP+ or 6-OHDA or by introducing the mutations or human genes implicated in inherited forms of PD.³⁵⁻⁴¹ These worm models exhibit PD-associated phenotypes including degeneration or loss of dopamine neurons, low dopamine levels, defects in dopamine-dependent behaviors, and movement defects.

Overexpression of human alpha-synuclein under the control of a DA neuron-specific promoter results in age-dependent neurodegeneration.⁴² Using this strain, over 30 strains of microbes were screened for prospective neuroprotective potential. Expression of human alpha-synuclein in the dopaminergic neurons induces complete degeneration and loss of the neurons by day 10 of adulthood. It was observed that when combined with 1 uM of Rotenone, the dopaminergic neuron loss is achieved more rapidly in 4 days. Rotenone is a broad-spectrum insecticide that has been demonstrated to induce PD-like symptoms in animal models accompanied by the selective destruction of DAergic neurons. In C. elegans, chronic exposure of rotenone caused dopaminergic neurodegeneration.⁴³ Rotenone acts by inhibiting mitochondrial respiratory complex I.⁴⁴ In the screen, the human alpha-synuclein animals were fed ad-libitum on a single strain of microbial lawn starting from the first larval stage and subjected to rotenone treatment at the fourth larval stage. After 60 hours of rotenone treatment, the animals were screened for survival of the anterior CEP (cephalic) dopaminergic neurons, which were visualized via co-expression of GFP driven in the dopaminergic neurons. While ˜75% of the worms fed on the control E. coli op50 had lost the CEP neurons, worms fed on Gluconoacetobacter EBT405 decreased CEP neurodegeneration (FIGS. 10A-10B).

References for Example 3

-   1. GBD 2015 Disease and Injury Incidence and Prevalence     Collaborators. Global, regional, and national incidence, prevalence,     and years lived with disability for 310 diseases and injuries,     1990-2015: a systematic analysis for the Global Burden of Disease     Study 2015. Lancet 388, 1545-1602 (2016). -   2. Pires, A. O. et al. Old and New Challenges in Parkinson's Disease     Therapeutics. Prog. Neurobiol. (2017).     doi:10.1016/j.pneurobio.0.2017.04.006 -   3. Nicklas, W. J., Vyas, I. & Heikkila, R. E. Inhibition of     NADH-linked oxidation in brain mitochondria by     1-methyl-4-phenyl-pyridine, a metabolite of the neurotoxin,     1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine. Life Sci. 36,     2503-2508 (1985). -   4. Ramsay, R. R., Salach, J. I., Dadgar, J. & Singer, T. P.     Inhibition of mitochondrial NADH dehydrogenase by pyridine     derivatives and its possible relation to experimental and idiopathic     parkinsonism. Biochem Biophys Res Commun 135, 269-275 (1986). -   5. Yoritaka, A. et al. Immunohistochemical detection of     4-hydroxynonenal protein adducts in Parkinson disease. Proceedings     of the National Academy of Sciences 93, 2696-2701 (1996). -   6. Floor, E. & Wetzel, M. G. Increased Protein Oxidation in Human     Substantia Nigra Pars Compacta in Comparison with Basal Ganglia and     Prefrontal Cortex Measured with an Improved Dinitrophenylhydrazine     Assay. J Neurochem 70, 268-275 (2002). -   7. Zhang, J. et al. Parkinson's disease is associated with oxidative     damage to cytoplasmic DNA and RNA in substantia nigra neurons.     Am. J. Pathol. 154, 1423-1429 (1999). -   8. Schapira, A. H. V. et al. MITOCHONDRIAL COMPLEX I DEFICIENCY IN     PARKINSON'S DISEASE. The Lancet 333,1269 (1989). -   9. Parker, W. D., Boyson, S. J. & Parks, J. K. Abnormalities of the     electron transport chain in idiopathic Parkinson's disease. Ann.     Neurol. 26, 719-723 (1989). -   10. Tieu, K. A guide to neurotoxic animal models of Parkinson's     disease. Cold Spring Harb Perspect Med 1, a009316-a009316 (2011). -   11. Moore, D. J., West, A. B., Dawson, V. L. & Dawson, T. M.     Molecular pathophysiology of Parkinson's disease. Annu. Rev.     Neurosci. 28, 57-87 (2005). -   12. Robinson, P. A. (2010). Understanding the molecular basis of     Parkinson's disease, identification of biomarkers and routes to     therapy. Expert Review of Proteomics, 7(4), 565-578. -   13. Dias, V., Junn, E., & Mouradian, M. M. The role of oxidative     stress in Parkinson's disease. Journal of Parkinson's Disease, 3(4),     461-491 (2013). -   14. Liu, X., Yamada, N., Maruyama, W., & Osawa, T. Formation of     dopamine adducts derived from brain polyunsaturated fatty acids:     mechanism for Parkinson disease. Journal of Biological Chemistry,     283(50), 34887-34895 (2008). -   15. Collier, T. J., Kanaan, N. M., & Kordower, J. H. Ageing as a     primary risk factor for Parkinson's disease: evidence from studies     of non-human primates. Nature Reviews. Neuroscience, 12(6), 359-366     (2011). -   16. GBD 2013 Mortality and Causes of Death Collaborators, Lancet     385,117 (2015). -   17. Federico, A., Cardaioli, E., Da Pozzo, P., Formichi, P.,     Gallus, G. N. and Radi, E. Mitochondria, oxidative stress and     neurodegeneration. J. Neurol. Sci, 322, 254-262 (2012). -   18. Winklhofer, K. F., and Haass, C. Mitochondrial dysfunction in     Parkinson's disease. Biochim. Biophys. Acta 1802, 29-44 (2010). -   19. Albers, D. S., and Flint Beal, M. Mitochondrial dysfunction and     oxidative stress in aging and neurodegenerative disease. In Advances     in Dementia Research (pp. 133-154) (2000). -   20. Andersen, J. K. Oxidative stress in neurodegeneration: cause or     consequence? Nature Reviews. Neuroscience, 10(7), S18-S25. (2004). -   21. Mukherjee, A., Biswas, A., & Das, S. K. Gut dysfunction in     Parkinson's disease. World Journal of Gastroenterology, 22(25),     5742-5752 (2016). -   22. Pellegrini, C., Colucci, R., Antonioli, L., Barocelli, E.,     Ballabeni, V., Bernardini, N., et al. Intestinal dysfunction in     Parkinson's disease: Lessons learned from translational studies and     experimental models. Neurogastroenterology & Motility, 28(12),     1781-1791 (2016). -   23. Kuo, Y.-M., Li, Z., Jiao, Y. N., Gaborit, A. K. Pani, B. M.     Orrison, B. G. Bruneau, B. I. Giasson, R. J. Smeyne, M. D. Gershon,     and R. L. Nussbaum. Extensive enteric nervous system abnormalities     in mice transgenic for artificial chromosomes containing Parkinson     disease-associated α-synuclein gene mutations precede central     nervous system changes. 19, 1633-1650 (2010). -   24. Noyce, A. J., Bestwick, J. P., Silveira-Moriyama, L., Hawkes, C.     H., Giovannoni, G., Lees, A. J and Schrag, A. Meta-analysis of early     nonmotor features and risk factors for Parkinson disease. 72,     893-901 (2012). -   25. Cersosimo, M. G and Benarroch, E. E. Pathological correlates of     gastrointestinal dysfunction in Parkinson's disease. 46, 559-564     (2012). -   26. Devos, D., Lebouvier, T., Lardeux, B. M., Biraud, Rouaud, T.,     Pouclet, H., E. Coron, Bruley des Varannes, S., Naveilhan, P.,     Nguyen, J.-M., Neunlist, M., and Derkinderen, P. Colonic     inflammation in Parkinson's disease. 50, 42-48 (2013). -   27. Braak, H., Rub, U., Gai, W. P and Del Tredici, K. Idiopathic     Parkinson's disease: possible routes by which vulnerable neuronal     types may be subject to neuroinvasion by an unknown pathogen. 110,     517-536 (2003). -   28. Hawkes, C. H., Del Tredici, K and Braak, H. Neuropathol.     Parkinson's disease: a dual-hit hypothesis. 33, 599-614 (2007). -   29. Hawkes, C. H., Del Tredici, K and Braak, H. Parkinson's disease:     the dual hit theory revisited. 1170, 615-622 (2009). -   30. Verbaan, D., Marinus, J., Visser, M., van Rooden, S. M.,     Stiggelbout, A. M., and van Hilten, J. J. Patient-reported autonomic     symptoms in Parkinson disease. Neurology 69, 333-341 (2007). -   31. Shannon, K. M., Keshavarzian, A., Dodiya, H. B., Jakate S., and     Kordower, J. H. Is alpha-synuclein in the colon a biomarker for     premotor Parkinson's disease? Evidence from 3 cases. Mov. Disord.     27, 716-719 (2012). -   32. Kieburtz, K and Wunderle, K. B. Parkinson's disease: evidence     for environmental risk factors. 28, 8-13 (2013). -   33. Caldwell, G. A., & Caldwell, K. A. Traversing a wormhole to     combat Parkinson's disease. Disease Models & Mechanisms, 1(1), 32-36     (2008). -   34. Nass, R., Hall, D. H., Miller, D. M. & Blakely, R. D.     Neurotoxin-induced degeneration of dopamine neurons in     Caenorhabditis elegans. Proceedings of the National Academy of     Sciences 99, 3264-3269 (2002). -   35. Lakso, M. et al. Dopaminergic neuronal loss and motor deficits     in Caenorhabditis elegans overexpressing human alpha-synuclein. J     Neurochem 86, 165-172 (2003). -   36. Ved, R. et al. Similar patterns of mitochondrial vulnerability     and rescue induced by genetic modification of alpha-synuclein,     parkin, and DJ-1 in Caenorhabditis elegans. J Biol Chem 280,     42655-42668 (2005). -   37. van Ham, T. J. et al. C. elegans model identifies genetic     modifiers of alpha-synuclein inclusion formation during aging. PLoS     Genet 4, e 1000027 (2008). -   38. Caldwell, G. A. & Caldwell, K. A. Traversing a wormhole to     combat Parkinson's disease. Dis Model Mech 1, 32-36 (2008). -   39. Harrington, A. J., Hamamichi, S., Caldwell, G. A. &     Caldwell, K. A. C. elegans as a model organism to investigate     molecular pathways involved with Parkinson's disease. Dev. Dyn. 239,     1282-1295 (2010). -   40. Braungart, E., Gerlach, M., Riederer, P., Baumeister, R. &     Hoener, M. C. Caenorhabditis elegans MPP+ model of Parkinson's     disease for high-throughput drug screenings. Neurodegener Dis 1,     175-183 (2004). -   41. Cao, S., Gelwix, C. C., Caldwell, K. A. & Caldwell, G. A.     Torsin-mediated protection from cellular stress in the dopaminergic     neurons of Caenorhabditis elegans. J. Neurosci. 25, 3801-3812     (2005). -   42. Hamamichi, S. et al. Hypothesis-based RNAi screening identifies     neuroprotective genes in a Parkinson's disease model. Proc Natl Acad     Sci USA 105, 728-733 (2008) -   43. Zhou, S., Wang, Z. & Klaunig, J. E. Caenorhabditis elegans     neuron degeneration and mitochondrial suppression caused by selected     environmental chemicals. Int J Biochem Mol Biol 4, 191-200 (2013). -   44. Gao, H.-M., Liu, B. & Hong, J.-S. Critical role for microglial     NADPH oxidase in rotenone-induced degeneration of dopaminergic     neurons. J. Neurosci. 23, 6181-6187 (2003).

Example 4: Treatment of Alzheimer's Disease

AD is a fatal neurodegenerative disease characterized by progressive decline in memory and cognitive functions. Early-onset familial AD associated with the mutations in APP or γ-secretase gene accounts for less than 5% of the all cases while 95% of the sporadic or late-onset AD has unknown etiology¹. The pathological hallmarks of AD are accumulation of extracellular senile plaques and intracellular neurofibrillary tangles (NFTs) in the AD patient's brain. The senile plaques consist of β-amyloid peptide (Aβ) as the primary component while NFTs consist of abnormal fibrillar forms of microtubule-associated protein tau as the primary component². Aβ accumulation and NFTs are thought to indicate neuronal dysfunction and impending neuronal demise².

Mitochondrial dysfunction and defects in energy metabolism have been consistently observed in human AD patients^(3,4). Aβ and tau pathologies are strongly associated with mitochondrial dysfunction in AD. Aβ and tau directly affect mitochondrial function causing impairment of ATP production, increased reactive oxygen species (ROS) production, decreased oxygen consumption, and decreased mitochondrial complex I and IV function⁵. Mitochondrial dysfunction is found to be an early event in AD. In the case of sporadic AD, progressive increase in oxidative stress with advancing age is shown to cause Aβ deposition and NFTs formation⁶. This could lead to a continuous cycle of events where the Aβ and tau exacerbates mitochondrial dysfunction leading to rapidly progressive AD symptoms. Thus, therapeutic efforts aimed at restoring mitochondrial function or protecting mitochondria against Aβ-induced damage or replenishing the mitochondrial numbers and function in the aging population is a promising route for identifying AD therapeutics.

C. elegans as a model is well-positioned to play an important role in AD-associated discoveries. Ortholog of genes associated with the cause of AD are conserved in C. elegans including amyloid precursor protein (APP) and tau. A number of worm models of AD have been generated by introducing the mutations or human genes implicated in AD⁷⁻⁹. These worm models exhibit AD-associated phenotypes including amyloid deposits, increased oxidative stress and progressive paralysis⁷⁻⁹. Further, impairment of electron transport chain function and mitochondrial dysfunction were found in the C. elegans AD models^(10,11), similar to those observed in AD patients. Further, these models have been used successfully in identifying neuroprotective compounds⁹.

About one third of the drugs used in the clinic today were initially isolated from plants or microbes. Though chemical synthesis of compounds has taken over the pharmaceutical industry as the source for identifying novel therapeutics, bioprospecting natural sources like plants and microbes continues to play important role as therapeutic agents. Recent studies have started to explore the human microbiome as a source of drugs.¹² The human body is home to a society of benign, symbiotic, commensal and pathogenic microbes collectively known as the microbiome. These microbes can modulate host brain function and behavior via the gut-brain axis and production of several metabolites such as GABA, glutamate and serotonin.

Dysfunction in the microbiome-derived metabolite signaling can contribute to neurological disorders including AD.^(13,14) In summary, the microbiome presents an untapped rich resource for mining novel neuroprotective compounds or live biotherapeutics that will be relevant for AD.

The inventors have developed a high-throughput screening (HTS) assay to rapidly prioritize “single” microbial species for identifying microbiome-based therapeutics for AD using C. elegans whole-animal model system. In the transgenic strains expressing AD-relevant human pathogenic Aβ or tau in all the neurons, it was found that mitochondrial unfolded protein response (as assessed by (UPRmt) reporter construct phsp-6::gfp) was turned on in many tissues, including the gut (FIGS. 11&12). hsp-6 encodes a mitochondrial matrix chaperone HSP70, which is specifically upregulated in response to impaired mitochondrial structure or function¹⁵ and can be assessed using the phsp-6::gfp strain in which the promoter of hsp-6 gene is tagged with GFP. These data are consistent with previous studies that show expression of Aβ in C. elegans results in the accumulation of abnormal mitochondria¹⁶ and muscle-specific expression of A 13 induced mitochondrial stress genes including hsp-6.¹¹ Expression of Aβ or tau in the neurons using the neuronal-specific (unc-119) promoter induces mitochondrial stress reporter expression (UPRmt) primarily in the gut (FIGS. 11 & 12), this response is cell-non-autonomous in nature. Similarly, neuron to gut cell-non-autonomous induction of UPRmt has been observed by other labs and proposed to function through neuropeptide and serotonin signaling pathways in C. elegans. ¹⁷⁻¹⁹

Interestingly, modulation of serotonin signaling is considered to be a potential symptomatic treatment for cognitive symptoms in AD.^(20,21) To determine whether the activation of UPRmt is a direct consequence of Aβ aggregates, transgenic worms expressing Aβ and phsp-6::gfp reporter were treated with Thioflavin T, which is an amyloid fibril-binding flavonoid shown to reduce Aβ aggregation in vivo and rescue the paralysis phenotype.²² It was found that in worms treated with Thioflavin T, the induction of UPRmt was reduced, indicating that the induction of UPRmt is directly due to Aβ aggregation. Thus, it is possible to screen for interventions that will reduce the UPRmt induction by modulating the Aβ aggregation or toxicity of Aβ on mitochondria.

For the screen, thirty microbial strains including the negative control bacteria E. coli OP50 were grown in appropriate culture media conditions and spotted onto standard nematode growth medium plates. ˜30 synchronized L1-larval-stage transgenic worm expressing Aβ 1-42 or tau in the pan-neurons were dropped onto the seeded plates and scored visually after 4 days under a fluorescent microscope for changes in phsp-6::gfp expression (FIG. 13). To synchronize worms, a bleach-prepping method was used, which also created germ-free animals that were fed on monocultures. The inventors screened for changes in the expression of phsp-6::gfp reporter and found that worms fed on Gluconobacter EBT 405 bacteria showed significant reduction in the expression of phsp-6::gfp induced by Aβ1-42 expressing or transgenic tau (FIGS. 11 & 12).

To evaluate the Aβ aggregation state in vivo, a transgenic strain expressing human Aβ3-42 conjugated in the body wall muscle²³ was used; EBT405 bacteria were tested on this model and found a significant reduction of A 13 deposits compared to transgenic worms fed on negative control bacteria (FIG. 14). This strain will be used to test the hits from the HTS screen for reduction of Aβ deposits.

To evaluate the ability of Gluconobacter EBT 405 to suppress Aβ-induced paralysis phenotype, the inventors used a strain that expresses full-length human Aβ1-42 peptide in body wall muscle cells²⁴. Shifting L4 or young adult animals from 20° C. to 25° C. causes paralysis in worms fed on the control bacteria while the time of onset of paralysis is significantly delayed in worms fed on Gluconobacter EBT 405.

References for Example 4

-   1. Masters, C. L. et al. Alzheimer's disease. Nat Rev Dis Primers 1,     15056 (2015). -   2. Nelson, P. T. et al. Correlation of Alzheimer disease     neuropathologic changes with cognitive status: a review of the     literature. J. Neuropathol. Exp. Neurol. 71, 362-381 (2012). -   3. Halliwell, B. Oxidative stress and neurodegeneration: where are     we now? J Neurochem 97, 1634-1658 (2006). -   4. Cheignon, C. et al. Oxidative stress and the amyloid beta peptide     in Alzheimer's disease. Redox Biol 14, 450-464 (2018). -   5. Müller, W. E., Eckert, A., Kurz, C., Eckert, G. P. & Leuner, K.     Mitochondrial dysfunction: common final pathway in brain aging and     Alzheimer's disease—therapeutic aspects. Mol. Neurobiol. 41, 159-171     (2010). -   6. Moreira, P. I., Carvalho, C., Zhu, X., Smith, M. A. & Perry, G.     Mitochondrial dysfunction is a trigger of Alzheimer's disease     pathophysiology. Biochim. Biophys. Acta 1802, 2-10 (2010). -   7. Link, C. D. C. elegans models of age-associated neurodegenerative     diseases: lessons from transgenic worm models of Alzheimer's     disease. Exp. Gerontol. 41, 1007-1013 (2006). -   8. Lublin, A. L. & Link, C. D. Alzheimer's disease drug discovery:     in vivo screening using Caenorhabditis elegans as a model for     β-amyloid peptide-induced toxicity. Drug Discov Today Technol 10,     e115-9 (2013). -   9. Chen, X., Barclay, J. W., Burgoyne, R. D. & Morgan, A. Using C.     elegans to discover therapeutic compounds for ageing-associated     neurodegenerative diseases. Chem Cent J 9, 65 (2015). -   10. Ng, L. F. et al. The mitochondria-targeted antioxidant MitoQ     extends lifespan and improves healthspan of a transgenic     Caenorhabditis elegans model of Alzheimer disease. Free Radic. Biol.     Med. 71, 390-401 (2014). -   11. Sorrentino, V. et al. Enhancing mitochondrial proteostasis     reduces amyloid-0 proteotoxicity. Nature 552, 187-193 (2017). -   12. Donia, M. S. & Fischbach, M. A. HUMAN MICROBIOTA. Small     molecules from the human microbiota. Science 349, 1254766-1254766     (2015). -   13. Sharon, G., Sampson, T. R., Geschwind, D. H. & Mazmanian, S. K.     The Central Nervous System and the Gut Microbiome. Cell 167, 915-932     (2016). -   14. Hill, J. M., Bhattacharjee, S., Pogue, A. I. & Lukiw, W. J. The     gastrointestinal tract microbiome and potential link to Alzheimer's     disease. Front Neurol 5, 43 (2014). -   15. Yoneda, T. et al. Compartment-specific perturbation of protein     handling activates genes encoding mitochondrial chaperones. J. Cell.     Sci. 117, 4055-4066 (2004). -   16. Fonte, V. et al. A glycine zipper motif mediates the formation     of toxic β-amyloid oligomers in vitro and in vivo. Mol Neurodegener     6, 61 (2011). -   17. Shao, L.-W., Niu, R. & Liu, Y. Neuropeptide signals cell     non-autonomous mitochondrial unfolded protein response. Cell Res.     26, 1182-1196 (2016). -   18. Durieux, J., Wolff, S. & Dillin, A. The cell-non-autonomous     nature of electron transport chain-mediated longevity. Cell 144,     79-91 (2011). -   19. Berendzen, K. M. et al. Neuroendocrine Coordination of     Mitochondrial Stress Signaling and Proteostasis. Cell 166,     1553-1563.e10 (2016). -   20. Ferrero, H., Solas, M., Francis, P. T. & Ramirez, M. J.     Serotonin 5-HT6Receptor Antagonists in Alzheimer's Disease:     Therapeutic Rationale and Current Development Status. CNS Drugs 31,     19-32 (2017). -   21. Claeysen, S., Bockaert, J. & Giannoni, P. Serotonin: A New Hope     in Alzheimer's Disease? ACS Chem Neurosci 6, 940-943 (2015). -   22. Alavez, S., Vantipalli, M. C., Zucker, D. J. S., Klang, I. M. &     Lithgow, G. J. Amyloid-binding compounds maintain protein     homeostasis during ageing and extend lifespan. Nature 472, 226-229     (2011). -   23. Link, C. D. et al. The beta amyloid peptide can act as a modular     aggregation domain. Neurobiol. Dis. 32, 420-425 (2008). -   24. McColl, G. et al. Utility of an improved model of amyloid-beta     (Aβ₁₋₄₂ toxicity in Caenorhabditis elegans for drug screening for     Alzheimer's disease. Mol Neurodegener 7, 57 (2012). 

1. A composition comprising a measured amount of bacteria that comprise and express nucleic acid sequences encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction derived therefrom.
 2. The composition of claim 1, which comprises a bacterium from the Acetobacteriaceae family, or an extract or fraction derived therefrom.
 3. The composition of claim 2, wherein the bacterium is Gluconobacter spp, Acetobacter spp., Gluconoacaetobacter spp., Acidomonas spp, Ameyamaea spp., Asaia spp., Granulibacter spp., Kozakia spp., Neoasaia spp., Neokomagataea spp., Saccharibacter spp., Swaminathania spp., or Tanticharoenia spp.
 4. The composition of claim 1, wherein one or more of the nucleic acid sequences are exogenous nucleic acid sequences.
 5. The composition of claim 1, wherein the measured amount of the bacteria is lyophilized.
 6. The composition of claim 1, wherein the composition further comprises one or more added bacterial metabolites selected from the group consisting of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.
 7. The composition of claim 1, wherein the composition is formulated as a food, a beverage, a feed composition, a probiotic, a nutritional supplement, or a pharmaceutical composition.
 8. The composition of claim 1, which further comprises a prebiotic.
 9. The composition of claim 1, further comprising a pharmaceutically acceptable carrier.
 10. The composition of claim 1, wherein the composition is formulated for oral administration.
 11. The composition of claim 10, wherein the composition is an enteric-coated formulation.
 12. A method for increasing cellular ATP production in at least one cell type of a subject in need thereof, the method comprising administering to the subject a composition comprising an amount of at least one non-pathogenic bacterium that comprises and expresses nucleic acid sequences encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or an extract or fraction thereof, effective to increase cellular ATP production in at least one cell type.
 13. The method of claim 12, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.
 14. The method of claim 12, wherein one or more of the nucleic acid sequences is exogenous to the bacterium.
 15. The method of claim 12, wherein the subject is human.
 16. The method of claim 12, wherein mitochondrial biogenesis is maintained or increased.
 17. The method of claim 12, wherein the activity of complex I and/or complex II of the mitochondrial electron transport chain is increased in the one or more cell types.
 18. The method of claim 12, wherein the administering increases mitochondrial membrane potential.
 19. The method of claim 12, wherein the administering increases one or more of: expression of peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α), and/or mitochondrial transcription factor A (TFAM); AMP-activated protein kinase (AMPK) phosphorylation level; nuclear respiratory factor-2 (Nrf2) protein level; PGC-1α mRNA level; TFAM mRNA level; mitochondrial DNA replication; mitochondrial DNA copy number (mtDNA); and expression of at least one mitochondrial β-oxidation enzyme.
 20. The method of claim 12, wherein cellular ATP production is increased by at least 10% compared to the cellular ATP production prior to administration of the composition.
 21. A method for making a bacterial extract, the method comprising culturing at least one bacterium that comprises and expresses nucleic acid sequences encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II in a medium comprising: (i) standard Lysogeny broth (1% tryptone, 0.5% yeast extract, and 1% sodium chloride) containing 1% glucose, (ii) standard Hestrin-Schramm broth (D-glucose 2%, 0.5% yeast extract, 0.5% peptone, 0.27% disodium phosphate, 0.115% citric acid) or (iii) CaCO₃ medium comprising 8% glucose, 0.5% yeast extract, 0.2% mannitol, 0.05% magnesium sulphate, and 10% calcium carbonate.
 22. The method of claim 21, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and 2,5-diketo-D-gluconic acid.
 23. A method for increasing the biogenesis of cellular mitochondria or peroxisomes, the method comprising administering to a subject, a composition comprising an amount of at least one bacterium that comprises and expresses nucleic acid sequences encoding membrane-bound PQQ-dependent glucose dehydrogenase (mGDH), ubiquinol-cytochrome c reductase iron-sulfur subunit, TonB-dependent receptor, carbon-nitrogen hydrolase, and ubiquinol oxidase subunit II, or a fraction or extract thereof, effective to increase the biogenesis of cellular mitochondria or peroxisomes.
 24. The method of claim 23, wherein the size and/or number of peroxisomes is increased.
 25. The method of claim 23, wherein mitochondrial activity is increased.
 26. The method of claim 23, wherein the at least one bacterium produces one or more of gluconic acid, 2-keto-gluconic acid, 5-keto-gluconic acid, and/or 2,5-diketo-D-gluconic acid. 